Expand Suite ID Tool IDs Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on BioBix Number of tools on CIRM-CFBP Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CorGAT Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on Lebanese University Galaxy Number of tools on MISSISSIPPI Number of tools on Mandoiu Lab Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) (usegalaxy.fr) Suite users (usegalaxy.fr) Suite runs (last 5 years) (usegalaxy.fr) Suite runs (usegalaxy.fr) Suite runs on main servers Suite runs (last 5 years) on main servers Suite users on main servers Suite users (last 5 years) on main servers Related Workflows Related Tutorials
2d_auto_threshold ip_threshold Automatic thresholding 2019-01-22 https://github.com/bmcv 0.25.0 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 130 154 3302 8913 5 5 29 29 12 12 607 607 0 0 0 0 9549 3938 171 147 https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/parameter-tuning, imaging/process-image-bioimageio, imaging/voronoi-segmentation
2d_feature_extraction ip_2d_feature_extraction 2D feature extraction 2019-01-08 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 52 67 2130 15217 0 0 0 0 4 4 167 167 0 0 0 0 15384 2297 71 56 https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1848?version=1 imaging/electrophoresis-gel-bands-image-analysis, imaging/hela-screen-analysis, imaging/voronoi-segmentation
2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules 2019-07-19 https://github.com/bmcv 0.0.1-4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34 49 514 7009 0 0 0 0 3 3 165 165 0 0 0 0 7174 679 52 37 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://workflowhub.eu/workflows/1508?version=1 imaging/hela-screen-analysis
2d_histogram_equalization ip_histogram_equalization 2d histogram equalization 2019-07-23 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 100 122 2565 2669 5 5 24 24 15 15 284 284 0 0 0 0 2977 2873 142 120 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1840?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/2D-spot-detection, imaging/imaging-introduction, imaging/parameter-tuning, imaging/yolo-segmentation-training
2d_simple_filter ip_filter_standard 2d simple filter 2019-01-22 https://github.com/bmcv 1.12.0 scipy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter scipy 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 131 2596 8178 5 5 23 23 15 15 484 484 0 0 0 0 8685 3103 151 127 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/parameter-tuning, imaging/voronoi-segmentation
2dnmrannotation 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra 2020-02-04 http://workflow4metabolomics.org 2.0.0+galaxy3 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 12 59 60 60 59 12 11
Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. 2015-10-02 https://rest.ensembl.org 1.0.0 python To update Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/main/tools/Ensembl-REST 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 62 87 322 2959 0 0 0 0 0 0 0 0 0 0 0 0 2959 322 87 62 https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3
abacas abacas Order and Orientate Contigs 2019-11-20 https://github.com/phac-nml/abacas 1.1 mummer 3.23 To update Assembly nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 3 3 3 2 2
anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion 2018-12-04 https://github.com/bmcv 0.4.0 medpy 0.4.0 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 924 964 0 0 0 0 0 0 0 0 0 0 0 0 964 924 3 2
apoc apoc Large-scale structural comparison of protein pockets 2017-07-04 https://sites.gatech.edu/cssb/apoc/ 1.0+galaxy1 apoc 1b16 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/apoc 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 6 9 9 3 3 26 26 0 0 0 0 0 0 0 0 35 35 9 9
apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy 2017-06-12 https://github.com/galaxy-genome-annotation/python-apollo apollo 4.2.13 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 393 403 5757 6363 3 3 9 9 0 0 0 0 0 0 0 0 6372 5766 406 396 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://workflowhub.eu/workflows/1554?version=1, https://workflowhub.eu/workflows/749?version=1 genome-annotation/apollo, genome-annotation/apollo-euk
askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ 2017-08-11 https://github.com/askomics/ askocli 0.5 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
askor_de askor_de AskoR links EdgeR and AskOmics 2018-04-06 https://github.com/askomics/askoR 0.2 bioconductor-limma 3.62.1 To update Transcriptomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 3 3 3 1 1
assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
background_removal background_removal Background removal filters using scikit-image 2024-07-12 https://github.com/bmcv 0.24.0 scikit-image To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 763 763 0 0 0 0 0 0 0 0 0 0 0 0 763 763 4 4
bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. 2020-04-28 https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 Up-to-date Sequence Analysis nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. 2022-03-03 https://www.cesgo.org/catibaric/ 1.1.0 To update Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 16 16 16 16 4 4
batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs 2024-04-30 https://github.com/galaxyproject/KegAlign 1.04.22 lastz 1.04.52 To update Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 37 313 313 0 0 0 0 0 0 0 0 313 313 37 37 https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615
bfconvert ip_convertimage Convert image 2019-07-22 https://github.com/bmcv 6.7.0 bftools 8.0.0 To update Imaging, Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert python-bioformats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 120 146 2087 2237 13 13 48 48 23 23 482 482 0 0 0 0 2767 2617 182 156 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1337?version=2, https://workflowhub.eu/workflows/1514?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/multiplex-tissue-imaging-TMA, imaging/voronoi-segmentation
binary2labelimage ip_binary_to_labelimage Binary 2 label image 2017-02-11 https://github.com/bmcv 0.6 giatools 0.4.1 To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 97 117 2363 3402 6 6 23 23 10 10 299 299 0 0 0 0 3724 2685 133 113 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/2D-spot-detection, imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation
binaryimage2points ip_binaryimage_to_points Binary Image to Points 2017-10-30 https://github.com/bmcv 0.1-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 729 758 0 0 0 0 0 0 0 0 0 0 0 0 758 729 2 1
bioformats2raw bf2raw Convert image to OME-Zarr 2023-11-02 https://github.com/Euro-BioImaging 0.7.0 To update Imaging, Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 109 109 0 0 0 0 0 0 0 0 0 0 0 0 109 109 7 7
biohansel biohansel Heidelberg and Enteritidis SNP Elucidation 2018-08-01 https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 To update Sequence Analysis nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input 2015-08-06 https://github.com/TGAC/earlham-galaxytools/ 0.2.0 python To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/main/tools/blast_parser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 133 146 769 942 0 0 0 0 0 0 0 0 0 0 0 0 942 769 146 133 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . 2021-10-05 https://github.com/Gaius-Augustus/BRAKER 2.1.6 To update Genome annotation genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 96 96 287 287 0 0 0 0 0 0 0 0 1 1 9 9 296 296 97 97
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camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos, CAMERA_findAdducts, CAMERA_findIsotopes, CAMERA_groupCorr, CAMERA_groupFWHM 2023-05-25 1.48.0 r-snow 0.4_1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 159 178 551 882 48 48 105 105 28 33 730 938 846 885 15960 16852 18777 17346 1144 1081 https://usegalaxy.fr/published/workflow?id=06fa7dd6eea42350, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=19e99a5c09c01bb7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=2ee479308227a926, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5ec8a143f82a8c90, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=98bb6a831a2b399d, https://usegalaxy.fr/published/workflow?id=b6311795ae10032b, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e6a55d00f1364794, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org.au/published/workflow?id=f9e5caaf08a450ec, https://usegalaxy.org.au/published/workflow?id=fa0243ff9b5ca997, https://usegalaxy.org/published/workflow?id=650f3eb7647b4508, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://workflowhub.eu/workflows/1584?version=1, https://workflowhub.eu/workflows/677?version=2 metabolomics/lcms, metabolomics/lcms-preprocessing
cfmid cfmid Competitive Fragmentation Modeling (CFM) 2019-03-07 https://sourceforge.net/p/cfm-id/ 33 cfm 33 Up-to-date Metabolomics computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1628?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/1658?version=1, https://workflowhub.eu/workflows/1793?version=1, https://workflowhub.eu/workflows/1855?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/1882?version=2, https://workflowhub.eu/workflows/246?version=4, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/354?version=1, https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/470?version=1, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/561?version=11, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/697?version=1 assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/ecoli_comparison, assembly/vgp_genome_assembly, computational-chemistry/cheminformatics, computational-chemistry/covid19-docking, ecology/phylogeny-data-prep, evolution/mtb_transmission, galaxy-interface/collections, galaxy-interface/workflow-automation, genome-annotation/gene-centric, genome-annotation/secondary-metabolite-discovery, imaging/hela-screen-analysis, imaging/parameter-tuning, introduction/galaxy-intro-ngs-data-managment, microbiome/clinical-mp-3-verification, microbiome/mgnify-amplicon, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-3-verification, proteomics/neoantigen-fragpipe-discovery, single-cell/bulk-deconvolution-evaluate, variant-analysis/aiv-analysis, variant-analysis/baculovirus-isolate-variation
color_deconvolution ip_color_deconvolution Color-deconvolution methods 2024-09-30 https://github.com/bmcv 0.9 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 7 9 132 135 0 0 0 0 0 0 0 0 0 0 0 0 135 132 9 7 https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b
colorize_labels colorize_labels Colorize label map 2024-03-12 https://github.com/bmcv 3.2.1 networkx To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 257 257 0 0 0 0 0 0 0 0 0 0 0 0 257 257 16 16 https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1 imaging/voronoi-segmentation
combine_assemblystats combine_stats Combine multiple Assemblystats datasets into a single tabular report 2017-11-08 https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.58 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
combine_json combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. 2018-03-02 0.1 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
combine_tabular_collection combine Combine Tabular Collection into a single file 2017-02-06 0.1 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
concat_channels ip_concat_channels Concatenate images 2017-10-30 https://github.com/bmcv 0.3-1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 15 43 87 0 0 0 0 0 0 0 0 0 0 0 0 87 43 15 12
concat_paired concat_fastqs Concatenate paired datasets 2019-12-16 https://github.com/phac-nml/concat 0.2 To update Text Manipulation nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI 2019-01-08 https://github.com/bmcv 0.0.4-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13 14 15194 17323 0 0 0 0 0 0 0 0 0 0 0 0 17323 15194 14 13 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis 2020-12-08 http://workflow4metabolomics.org 1.0.1+galaxy2 r-batch 1.1_4 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 241 241 241 241 57 57
count_objects ip_count_objects Count Objects 2019-01-08 https://github.com/bmcv 0.0.5-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79 96 1176 1241 8 8 24 24 7 7 183 183 0 0 0 0 1448 1383 111 94 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/imaging-introduction, imaging/voronoi-segmentation
crop_image ip_crop_image Crop image 2025-06-06 https://github.com/bmcv 0.4.1 giatools 0.4.1 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image giatools giatools Tools required for Galaxy Image Analysis 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA (18S) and gp60 markers. 2020-10-14 https://github.com/phac-nml/CryptoGenotyper 1.5.0 cryptogenotyper 1.5.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 31 31 12430 12430 0 0 0 0 0 0 0 0 0 0 0 0 12430 12430 31 31 https://usegalaxy.eu/published/workflow?id=07865c770825c54a, https://usegalaxy.eu/published/workflow?id=280877e42b09f49f, https://usegalaxy.eu/published/workflow?id=3d7659452e3af984, https://usegalaxy.eu/published/workflow?id=4ba4da05a7696923, https://usegalaxy.eu/published/workflow?id=aefe927f13bc9374, https://usegalaxy.eu/published/workflow?id=f7558edf450e781f
csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files 2019-08-23 https://bioinf.shenwei.me/csvtk/ 0.20.0 csvtk 0.31.0 To update Text Manipulation nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0 6 0 1 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 350 350 18 18 130 130 480 480 25 25
curve_fitting ip_curve_fitting Polynomial curve fitting to data points 2021-07-22 https://github.com/BMCV/galaxy-image-analysis 0.0.3-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 4 4 https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1 imaging/detection-of-mitoflashes
detection_viz ip_detection_viz Detection Visualization 2017-10-30 https://github.com/bmcv 0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 9 6 49 0 0 0 0 0 0 0 0 0 0 0 0 49 6 9 6
ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species 2018-12-21 https://github.com/phac-nml/ecoli_serotyping 2.0.0 ectyper 2.0.0 Up-to-date Sequence Analysis Sequence assembly, Read pre-processing, Variant calling Sequence assembly, Read pre-processing, Variant calling Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper ectyper ECTyper Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0) 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 218 218 30463 30463 1 1 10 10 0 0 0 0 0 0 0 0 30473 30473 219 219 https://usegalaxy.eu/published/workflow?id=b90585626a793502
ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit 2016-06-01 https://etetoolkit.org/ 3.1.3 ete3 3.1.1 To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 30 39 279 1030 0 0 0 0 0 0 0 0 2 2 13 13 1043 292 41 32
export_to_cluster export_to_cluster Export datasets to cluster 2016-01-18 https://github.com/TGAC/earlham-galaxytools/ 0.1.0 python To update Data Export earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/export_to_cluster 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format 2017-10-11 https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta_extract fa-extract-sequence extract single fasta from multiple fasta file 2016-10-26 https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract 1.1.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 10 0 0 0 0 107 181 923 1827 0 0 0 0 1837 923 182 107
fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report 2017-10-11 https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 2018-04-11 https://github.com/tderrien/FEELnc 0.1 perl-bioperl 1.7.8 To update Convert Formats genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feht feht Automatically identify makers predictive of groups. 2017-10-11 https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds 2017-10-12 https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gafa gafa Gene Align and Family Aggregator 2016-12-15 https://github.com/TGAC/Aequatus 0.4.1 python To update Visualization earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 6 5 47 0 0 0 0 0 0 0 0 0 0 0 0 47 5 6 4 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
gblocks gblocks Gblocks 2018-04-11 https://www.biologiaevolutiva.org/jcastresana/Gblocks/Gblocks_documentation.html 0.91b gblocks 0.91b Up-to-date Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gblocks 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 87 87 661 661 6 6 36 36 697 697 93 93
gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs 2023-03-15 https://github.com/p2m2/p2m2tools 0.2.1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor 2021-09-16 0.1.0 openjdk To update Metabolomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io 2021-09-17 https://genenotebook.github.io 0.4.18 genoboo 0.4.18 Up-to-date Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 8 8 0 0 0 0 0 0 0 0 9 9 354 354 362 362 13 13
genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data 2019-09-12 https://sourceforge.net/projects/genform/ genform r8 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 4 3 68 0 0 0 0 0 0 0 0 0 0 0 0 68 3 4 2
get_pairs get_pairs Separate paired and unpaired reads from two fastq files 2018-09-10 0.3 python To update Fastq Manipulation genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
getmlst getmlst Download MLST datasets by species from pubmlst.org 2015-12-03 0.1.4.1 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gnali gnali A tool to find nonessential, loss-of-function gene variants 2020-03-30 https://github.com/phac-nml/gnali/ 1.1.0 gnali 1.1.0 Up-to-date Variant Analysis nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow 2017-03-15 https://github.com/TGAC/earlham-galaxytools/ 0.4.3 python To update Convert Formats earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gstf_preparation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 20 21 404 0 0 0 0 0 0 0 0 0 0 0 0 404 21 20 14
hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph 2015-08-05 https://github.com/douglasgscofield/hcluster 0.5.1.1 hcluster_sg 0.5.1 To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 69 147 303 0 0 0 0 0 0 0 0 0 0 0 0 303 147 69 59 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids 2015-08-12 https://github.com/TGAC/earlham-galaxytools/ 0.3.0 python To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg_parser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 27 41 298 0 0 0 0 0 0 0 0 0 0 0 0 298 41 27 19 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
helixer helixer Gene calling with Deep Neural Networks 2023-06-14 https://github.com/weberlab-hhu/Helixer 0.3.3 To update Genome annotation Gene prediction, Genome annotation Gene prediction, Genome annotation Sequence analysis, Gene transcripts Sequence analysis, Gene transcripts genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer helixer Helixer Deep Learning to predict gene annotations 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 161 161 1024 1024 56 56 184 184 51 51 385 385 25 25 363 363 1956 1956 293 293 https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1746?version=1 genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer
hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. 2015-12-10 1.0.1 hivtrace 1.5.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
image_info ip_imageinfo Extracts image metadata 2019-07-19 https://github.com/bmcv 5.7.1 bftools 8.0.0 To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info python-bioformats 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 100 122 436 887 0 0 0 0 16 16 206 206 0 0 0 0 1093 642 138 116 https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1848?version=1 imaging/electrophoresis-gel-bands-image-analysis, imaging/imaging-introduction, imaging/voronoi-segmentation
image_math image_math Process images using arithmetic expressions 2024-03-09 https://github.com/bmcv 1.26.4 numpy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 380 380 0 0 0 0 1 1 11 11 0 0 0 0 391 391 17 17 https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1730?version=1 imaging/process-image-bioimageio, imaging/voronoi-segmentation
image_registration_affine ip_image_registration Intensity-based Image Registration 2020-12-29 https://github.com/bmcv 0.0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 17 17 0 0 0 0 0 0 0 0 0 0 0 0 17 17 5 5
imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes 2019-03-08 https://github.com/bmcv 0.1-2 pandas To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 14 19734 21898 0 0 0 0 0 0 0 0 0 0 0 0 21898 19734 14 11 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
influx_si influx_si metabolic flux estimation based on [in]stationary labeling 2020-04-17 https://github.com/sgsokol/influx 7.0.1 influx_si 7.4.1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 18 18 18 18 2 2 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
influx_si_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows 2024-02-09 https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ 1.0.2 influx-si-data-manager 1.1.1 To update Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 9 9 9 9 1 1 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
intensity_checks intens_check Statistical measures, number of missing values and mean fold change for metabolomics data. 2025-05-14 https://workflow4metabolomics.org/ 2.0.1 r-base To update Metabolomics melpetera https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/intensity_check 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 46 229 233 22 22 76 76 0 0 0 0 372 376 8696 8857 9166 9001 444 437 https://usegalaxy.eu/published/workflow?id=3e2718f1ba1a22be, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=18b2f77f2915adc7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=49e59327f299e9f7, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5bfbe77fd6b37c45, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=7e9dcb13f95f9567, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e3d00bdef9addd7c, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org/published/workflow?id=650f3eb7647b4508, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://workflowhub.eu/workflows/677?version=2 metabolomics/lcms-dataprocessing, metabolomics/lcms-preprocessing
ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO 2019-10-02 https://github.com/rietho/IPO 1.10.0 bioconductor-ipo 1.32.0 To update Metabolomics lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments 2021-07-12 https://github.com/llegregam/Isoplot 1.3.1 jinja2 To update Metabolomics, Visualization workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 5 5 0 0 0 0 0 0 0 0 11 11 132 132 137 137 14 14 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
jbrowse_to_container jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container 2016-11-08 https://jbrowse.org python To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. 2017-04-10 0.3.0 kaptive 3.1.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes 2017-03-13 2.3 kat 2.4.2 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. 2017-02-06 2.3 kat 2.4.2 To update nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 2024-08-29 https://github.com/galaxyproject/KegAlign 0.1.2.8 kegalign-full 0.1.2.8 Up-to-date Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 52 228 228 0 0 0 0 0 0 0 0 228 228 52 52 https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615
kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file 2023-07-10 https://github.com/workflow4metabolomics/tools-metabolomics 1.0.0 click To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
label_to_binary label_to_binary Convert label map to binary image 2024-03-13 https://github.com/bmcv 1.26.4 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 104 104 0 0 0 0 0 0 0 0 0 0 0 0 104 104 1 1
labelimage2points ip_labelimage_to_points Label Image to Points 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 106 142 0 0 0 0 0 0 0 0 0 0 0 0 142 106 3 2
landmark_registration ip_landmark_registration Landmark Registration 2019-02-04 https://github.com/bmcv 0.1.0-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 19 871 1035 6 6 7 7 0 0 0 0 0 0 0 0 1042 878 25 22 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence 2018-06-06 http://logol.genouest.org/web/app.php/logol 1.7.8 logol 1.7.8 Up-to-date Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lotus2 lotus2 LotuS2 OTU processing pipeline 2021-05-13 https://lotus2.earlham.ac.uk/ 2.32 lotus2 2.34.1 To update Metagenomics Sequence feature detection, DNA barcoding Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Metagenomics, Taxonomy, Microbial ecology earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/main/tools/lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 249 249 1979 1979 0 0 0 0 22 22 417 417 2 2 5 5 2401 2401 273 273 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon
mahotas_features ip_mahotas_features Compute image features using mahotas. 2024-09-30 https://github.com/luispedro/mahotas 0.7-2 mahotas To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features mahotas-feature-computation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 7 10 45 0 0 0 0 0 0 0 0 0 0 0 0 45 10 7 6
mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome 2019-11-19 https://github.com/phac-nml/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 To update Sequence Analysis nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network 2018-06-11 http://bioasp.github.io/meneco/ 1.5.2 meneco 1.5.2 Up-to-date Systems Biology genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image 2019-01-08 https://github.com/bmcv 0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 3 1 25 0 0 0 0 0 0 0 0 0 0 0 0 25 1 3 1
metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) 2018-03-25 https://github.com/computational-metabolomics/metfrag-galaxy 2.4.5+galaxy3 metfrag 2.4.5 To update Metabolomics computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 22 25 109 206 0 0 0 0 0 0 0 0 87 88 452 457 663 561 113 109 https://usegalaxy.fr/published/workflow?id=bcd348178335a19b
metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag 2020-06-30 https://github.com/computational-metabolomics/metfrag-galaxy 2.4.5+galaxy0 metfrag 2.4.5 To update Metabolomics computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 64 64 0 0 0 0 0 0 0 0 0 0 0 0 64 64 16 16
miranda miranda Finds potential target sites for miRNAs in genomic sequences 2015-10-30 https://github.com/hacktrackgnulinux/miranda 3.3a+galaxy1 miranda 3.3a To update RNA earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 123 2555 7459 0 0 0 0 0 0 0 0 23 23 27 27 7486 2582 146 123
miranda2asko miranda2asko Converts miRanda output into AskOmics format 2018-04-12 0.2 perl To update Convert Formats genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model 2022-05-16 http://workflow4metabolomics.org 3.1.0+galaxy1 r-lme4 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 39 39 368 368 369 369 40 40
mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies 2018-04-30 https://github.com/phac-nml/mob-suite 3.1.9 mob_suite 3.1.9 Up-to-date Sequence Analysis Clustering, Sequence analysis Clustering, Sequence analysis Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements, Genomics Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite mob_suite mob_suite MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location. 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 620 620 162457 162457 1 1 42 42 199 199 66525 66525 12 12 58 58 229082 229082 832 832 https://workflowhub.eu/workflows/407?version=1
morphological_operations morphological_operations Apply morphological operations to images 2024-03-08 https://github.com/bmcv 1.12.0 scipy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations scipy 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 298 298 0 0 0 0 0 0 0 0 0 0 0 0 298 298 1 1
mrbayes mrbayes A program for the Bayesian estimation of phylogeny. 2015-12-04 1.0.2 mrbayes 3.2.7 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 4 4 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 4 4
ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. 2022-03-15 http://workflow4metabolomics.org 2.2.1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 157 157 157 157 10 10
msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data 2019-05-24 https://github.com/computational-metabolomics/mspurity-galaxy 1.28.0 bioconductor-mspurity 1.32.0 To update Metabolomics computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 20 21 591 900 0 0 0 0 0 0 0 0 147 148 11336 11552 12452 11927 169 167 https://usegalaxy.fr/published/workflow?id=6babfa7409467035, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=cca13353d553319e
msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data 2019-09-24 https://github.com/computational-metabolomics/mspurity-galaxy 0.0.2 To update Metabolomics tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. 2018-09-28 https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base To update Sequence Analysis nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML 2024-09-20 https://rdrr.io/bioc/mzR/ 1.0.0+galaxy1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2721 2721 2721 2721 8 8
ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) 2024-08-19 https://github.com/ncbi/egapx 0.4.1 To update Genome annotation richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7 7 49 49 1037 1037 0 0 0 0 0 0 0 0 1044 1044 51 51 https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://usegalaxy.org/published/workflow?id=ce488732866ba48f, https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6
ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. 2024-02-23 https://github.com/ncbi/fcs 0.5.0 To update Sequence Analysis richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 12 12 374 374 9268 9268 0 0 0 0 0 0 0 0 9280 9280 375 375 https://usegalaxy.org/published/workflow?id=927b8f90ad9603a7, https://workflowhub.eu/workflows/645?version=14 sequence-analysis/ncbi-fcs
nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation 2019-07-30 http://workflow4metabolomics.org 3.0.0+galaxy1 libgfortran To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 6 14 51 0 0 0 0 0 0 0 0 48 51 479 508 559 493 57 53
nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction 2019-07-29 http://workflow4metabolomics.org r-ggplot2 2.2.1 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 5 6 87 146 0 0 0 0 5 5 343 429 92 96 2370 2469 3044 2800 107 102
normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data 2019-07-30 http://workflow4metabolomics.org 1.0.7+galaxy2 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 50 53 182 242 0 0 0 0 14 15 243 289 315 329 3350 3424 3955 3775 397 379 https://usegalaxy.eu/published/workflow?id=3e2718f1ba1a22be, https://usegalaxy.fr/published/workflow?id=7e9dcb13f95f9567 metabolomics/lcms-dataprocessing
openlabcds2csv openlabcds2csv Creates a summary of several "Internal Standard Report" OpenLabCDS results. 2021-10-28 0.1.0 openjdk To update Metabolomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
orientationpy orientationpy Compute image orientation 2024-03-12 https://github.com/bmcv 0.2.0.4 orientationpy 0.2.0.4 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy orientationj 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 105 105 0 0 0 0 0 0 0 0 0 0 0 0 105 105 2 2
overlay_images ip_overlay_images Overlay two images 2022-02-26 https://github.com/BMCV/galaxy-image-analysis 0.0.4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 56 56 466 466 4 4 19 19 2 2 303 303 0 0 0 0 788 788 62 62 https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 imaging/2D-spot-detection, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation
pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages 2020-05-01 https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3.1 To update Sequence Analysis nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 595 595 7737 7737 416 416 9068 9068 277 277 3099 3099 12 12 603 603 20507 20507 1300 1300 https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/1391?version=1, https://workflowhub.eu/workflows/155?version=6 galaxy-interface/workflow-automation, variant-analysis/sars-cov-2-variant-discovery
patrist patrist Extract Patristic Distance From a Tree 2019-12-14 https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 0.1.2 python To update Phylogenetics nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes 2021-11-03 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 2.1 To update Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 6 6 6 6 1 1
permutate_axis ip_permutate_axis Permutates axes 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2 0 42 0 0 0 0 0 0 0 0 0 0 0 0 42 0 2 0
physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes 2022-09-26 physiofit.readthedocs.io 3.4.0 physiofit 3.4.0 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 28 28 28 28 2 2 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
physiofit_manager physiofit_data_manager Handling of physiofit input files 2022-11-03 physiofit.readthedocs.io 1.0.1 physiofit_data_manager 1.0.1 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 9 9 9 9 1 1 https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac
plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images 2024-06-19 https://github.com/bmcv 1.8.1 plant-seg To update Imaging Network analysis, Quantification, Microscope image visualisation Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plasmid_profiler plasmid_profiler Explores plasmid content in WGS data 2016-11-07 0.1.6 r To update nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plasmidspades plasmidspades Genome assembler for assemblying plasmid 2016-06-06 1.1 spades 4.2.0 To update Assembly nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plotheatmap plotheatmap Plot heatmap of gene expression data 2017-07-04 https://github.com/TGAC/earlham-galaxytools/ 1.0 bioconductor-preprocesscore 1.68.0 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads 2020-03-24 https://github.com/phe-bioinformatics/PneumoCaT 1.2.1 pneumocat 1.2.1 Up-to-date Variant Analysis nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
points2labelimage ip_points_to_label Points to label image 2017-10-30 https://github.com/bmcv 0.4.1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 46 77 0 0 0 0 0 0 0 0 0 0 0 0 77 46 3 2 https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1848?version=1 imaging/2D-spot-detection, imaging/electrophoresis-gel-bands-image-analysis
points_association_nn ip_points_association_nn Association of points in consecutive frames 2021-07-22 https://github.com/BMCV/galaxy-image-analysis 0.0.3-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 6 6 https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1 imaging/detection-of-mitoflashes
projective_transformation ip_projective_transformation Projective transformation 2018-12-07 https://github.com/bmcv 0.1.2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 6 21 86 0 0 0 0 0 0 0 0 0 0 0 0 86 21 6 3 https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890
projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates 2018-12-07 https://github.com/bmcv 0.1.1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 20 19258 21493 0 0 0 0 0 0 0 0 0 0 0 0 21493 19258 20 15 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them 2019-12-14 https://github.com/phac-nml/promer 1.2 python To update Assembly nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. 2018-04-06 https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime2 qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats 2022-08-26 https://github.com/biocore/deblur 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 40 40 225 225 24 24 78 78 9 9 177 177 1 1 8 8 488 488 74 74
qiime2 qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac 2022-08-26 https://github.com/qiime2/q2-diversity-lib 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 12 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 4 4 33 33 8 8 47 47 6 6 2850 2850 2 2 3 3 2933 2933 20 20 https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927
qiime2 qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads 2022-08-26 https://github.com/qiime2/q2-quality-control 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 6 6 11 11 105 105 4 4 11 11 0 0 0 0 122 122 19 19
qiime2 qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds 2022-08-26 https://github.com/qiime2/q2-phylogeny 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 12 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 167 167 880 880 93 93 338 338 66 66 373 373 13 13 91 91 1682 1682 339 339 https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05
qiime2 qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate 2022-08-26 https://github.com/qiime2/q2-metadata 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 331 331 2227 2227 292 292 1317 1317 94 94 744 744 39 39 269 269 4557 4557 756 756 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3
qiime2 qiime2__quality_filter__q_score 2022-08-26 https://github.com/qiime2/q2-quality-filter 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 25 25 55 55 16 16 39 39 7 7 90 90 13 13 21 21 205 205 61 61
qiime2 qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp 2022-08-26 https://github.com/qiime2/q2-fragment-insertion 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 16 16 81 81 7 7 59 59 1 1 6 6 2 2 2 2 148 148 26 26 https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405
qiime2 qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__normalize, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose 2022-08-26 https://github.com/qiime2/q2-feature-table 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 17 17 17 17 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 298 298 5335 5335 203 203 1938 1938 95 95 2932 2932 28 28 591 591 10796 10796 624 624 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3
qiime2 qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global 2022-08-26 https://github.com/qiime2/q2-feature-classifier 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 10 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 325 325 3046 3046 232 232 1256 1256 88 88 1282 1282 28 28 178 178 5762 5762 673 673 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927
qiime2 qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask 2022-08-26 https://github.com/qiime2/q2-alignment 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 67 67 390 390 35 35 78 78 16 16 114 114 14 14 69 69 651 651 132 132
qiime2 qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap 2022-08-26 https://github.com/qiime2/q2-diversity 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 21 21 22 21 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 135 135 3770 3770 88 88 2286 2286 60 60 1211 1211 26 26 360 360 7627 7627 309 309 https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318
qiime2 qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate 2022-08-26 https://github.com/qiime2/q2-composition 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 2 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 26 26 388 388 31 31 256 256 8 8 325 325 9 9 89 89 1058 1058 74 74
qiime2 qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single 2022-08-26 https://github.com/qiime2/q2-cutadapt 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 73 73 364 364 69 69 273 273 7 7 213 213 3 3 31 31 881 881 152 152
qiime2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single 2022-08-26 http://benjjneb.github.io/dada2/ 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 319 319 2670 2670 253 253 1230 1230 79 79 843 843 29 29 182 182 4925 4925 680 680 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3
qiime2 qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts 2022-08-26 https://github.com/qiime2/q2-demux 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 289 289 1358 1358 251 251 1071 1071 91 91 1146 1146 28 28 127 127 3702 3702 659 659 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://workflowhub.eu/workflows/893?version=3
qiime2 qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility 2022-08-26 https://github.com/qiime2/q2-longitudinal 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 11 11 11 11 0 0 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 12 12 63 63 7 7 60 60 6 6 142 142 2 2 8 8 273 273 27 27
qiime2 qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot 2022-08-26 http://biocore.github.io/emperor/build/html/index.html 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 42 42 142 142 34 34 198 198 15 15 195 195 9 9 27 27 562 562 100 100
qiime2 qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize 2022-08-26 https://github.com/qiime2/q2-sample-classifier 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 15 15 15 15 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 5 5 30 30 17 17 47 47 5 5 6 6 1 1 4 4 87 87 28 28
qiime2 qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table 2022-08-26 https://github.com/qiime2/q2-taxa 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 266 266 2747 2747 159 159 1008 1008 78 78 690 690 22 22 236 236 4681 4681 525 525 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4
qiime2 qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d 2024-10-30 https://github.com/qiime2/q2-vizard 0.0.1.dev0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 20 20 0 0 0 0 0 0 0 0 0 0 0 0 20 20 5 5
qiime2 qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_bv_brc_genome_features, qiime2__rescript__get_bv_brc_genomes, qiime2__rescript__get_bv_brc_metadata, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_midori2_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment 2024-04-25 https://github.com/nbokulich/RESCRIPt 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 6 6
qiime2 qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref 2022-08-26 https://github.com/qiime2/q2-vsearch 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 8 8 8 8 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 31 31 409 409 18 18 280 280 5 5 24 24 10 10 77 77 790 790 64 64
qiime2 qiime2__stats__alpha_group_significance, qiime2__stats__collate_stats, qiime2__stats__facet_across, qiime2__stats__facet_within, qiime2__stats__mann_whitney_u, qiime2__stats__mann_whitney_u_facet, qiime2__stats__plot_rainclouds, qiime2__stats__prep_alpha_distribution, qiime2__stats__wilcoxon_srt, qiime2__stats__wilcoxon_srt_facet 2024-10-30 https://github.com/qiime2/q2-stats 2025.7.0+q2galaxy.2025.7.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime2 qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq 2022-08-26 https://qiime2.org 2025.7.0+dist.h44bd78f6 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 2 2 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 636 636 61165 61165 813 813 58124 58124 228 228 10152 10152 62 62 2237 2237 131678 131678 1739 1739 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318, https://workflowhub.eu/workflows/893?version=3
quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies 2017-10-05 https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0 12 0 12 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 182 183 15277 15540 8 8 39 39 15579 15316 191 190
rdeval rdeval, rdeval_report rdeval is a General purpose, multithreaded read analysis and manipulation tool. 2025-02-17 https://github.com/vgl-hub/rdeval 0.0.7 rdeval 0.0.7 Up-to-date Assembly richard-burhans https://github.com/vgl-hub/rdeval https://github.com/richard-burhans/galaxytools/tree/main/tools/rdeval 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 223 223 0 0 0 0 0 0 0 0 223 223 15 15 https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://usegalaxy.org/published/workflow?id=beefb67de2b0728c, https://workflowhub.eu/workflows/632?version=12
rdock rdock Docking ligands to proteins and nucleic acids 2016-12-14 https://rdock.github.io/ 1.0 rDock 2013.1 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/rdock 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. 2018-01-31 https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 149 149 3315 3315 164 164 992 992 0 0 0 0 14 14 4334 4334 8641 8641 327 327 https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/1043?version=11
repeat_channels repeat_channels Convert single-channel to multi-channel image 2024-04-25 https://github.com/bmcv 1.26.4 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 101 101 0 0 0 0 0 0 0 0 0 0 0 0 101 101 15 15 https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1 imaging/voronoi-segmentation
repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. 2023-11-01 https://github.com/repeatexplorer/repex_tarean 2.3.8 To update Genome annotation gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 369 369 0 0 0 0 0 0 0 0 0 0 0 0 369 369 83 83
replace_chromosome_names replace_chromosome_names Replace chromosome names 2017-05-18 https://github.com/dpryan79/ChromosomeMappings/ 0.1 python To update Text Manipulation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/replace_chromosome_names 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 93 582 749 0 0 0 0 0 0 0 0 0 0 0 0 749 582 93 54
rfove rfove Perform segmentation region-based fitting of overlapping ellipses 2023-11-12 https://sites.google.com/site/costaspanagiotakis/research/cs 2023.11.12 To update Imaging Image analysis Image analysis Cell biology, Biomedical science, Imaging Cell biology, Biomedical science, Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 15 15 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7
scale_image ip_scale_image Scale image 2018-12-07 https://github.com/bmcv 0.18.3 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 20 751 870 0 0 0 0 0 0 0 0 0 0 0 0 870 751 20 17 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc
segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 2024-04-15 https://github.com/gsneha26/SegAlign 0.1.2.7 segalign-galaxy 0.1.2.7 Up-to-date Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 123 468 468 0 0 0 0 0 0 0 0 468 468 123 123
segmetrics ip_segmetrics Image segmentation and object detection performance measures 2022-10-07 https://github.com/bmcv 1.4 segmetrics 1.5 To update Imaging Image analysis Image analysis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures segmetrics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 88 88 0 0 0 0 0 0 0 0 0 0 0 0 88 88 3 3 https://workflowhub.eu/workflows/1517?version=1 imaging/parameter-tuning
seqtk_nml seqtk_nml_sample Tool to downsample fastq reads 2017-09-19 https://github.com/lh3/seqtk 1.0.1 seqtk 1.5 To update Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sistr_cmd sistr_cmd SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd 1.1.3 sistr_cmd 1.1.3 Up-to-date Sequence Analysis Genome assembly, Visualisation, Multilocus sequence typing Genome assembly, Visualisation, Multilocus sequence typing Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology nml https://github.com/phac-nml/sistr_cmd https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd SISTR SISTR The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 395 397 5345 5466 0 0 0 0 91 95 907 1010 0 0 0 0 6476 6252 492 486 https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1
skyline2isocor skyline2isocor Converting skyline output to IsoCor input 2024-02-07 https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor 1.0.0 skyline2isocor 1.0.0 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 10 10 149 149 150 150 11 11
slice_image ip_slice_image Slice image 2017-10-30 https://github.com/bmcv 0.3-4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 6 4 104 0 0 0 0 1 1 48 48 0 0 0 0 152 52 7 4
smalt smalt SMALT aligns DNA sequencing reads with a reference genome. 2017-09-19 http://www.sanger.ac.uk/science/tools/smalt-0 0.7.6 smalt 0.7.6 Up-to-date Sequence Analysis nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smart_domains smart_domains SMART domains 2017-05-12 https://smart.embl.de/ 0.1.0 perl-bioperl 1.7.8 To update Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smart_domains 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smina smina Scoring and Minimization with smina 2017-07-07 https://sourceforge.net/projects/smina/ 1.0 smina 2017.11.9 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smina 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 18 501 501 14 14 50 50 0 0 0 0 0 0 0 0 551 551 32 32
spades_fasta_header_fixer spades_header_fixer Fixes Spades Fasta ids 2019-12-18 https://github.com/phac-nml/galaxy_tools 1.1.2+galaxy1 sed To update Fasta Manipulation nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. 2023-03-16 https://github.com/HCGB-IGTP/spaTyper 0.3.3 spatyper 0.3.3 Up-to-date Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
split_image ip_split_image Split image along axes 2025-03-07 https://github.com/bmcv 2.2.3 numpy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 232 232 0 0 0 0 0 0 0 0 0 0 0 0 232 232 17 17 https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1848?version=1 imaging/electrophoresis-gel-bands-image-analysis, imaging/process-image-bioimageio
split_labelmap ip_split_labelmap Split Labelmaps 2018-12-11 https://github.com/bmcv 0.2-3 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 4 113 155 0 0 0 0 0 0 0 0 0 0 0 0 155 113 4 2
spolpred spolpred A program for predicting the spoligotype from raw sequence reads 2015-12-14 1.0.1 spolpred To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence 2021-07-20 https://github.com/BMCV/galaxy-image-analysis 0.1 giatools 0.4.1 To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 93 93 0 0 0 0 0 0 0 0 0 0 0 0 93 93 7 7 https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1, https://workflowhub.eu/workflows/1528?version=1 imaging/2D-spot-detection, imaging/detection-of-mitoflashes
srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 2015-12-02 0.3.7 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 https://workflowhub.eu/workflows/407?version=1
staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2018-05-10 https://github.com/phac-nml/staramr 0.11.0 staramr 0.11.1 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2921 3072 31443 33124 2130 2130 14763 14763 1173 1182 8989 9237 97 97 9838 9838 66962 65033 6481 6321 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore
stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) 2016-10-19 1.1.0 stringMLST 0.6.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_plasmid_profiler Plasmid Profiler suite defining all dependencies for Plasmid Profiler 2016-11-07 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_qiime2_core 2022-08-29 To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images 2023-06-20 https://github.com/bmcv 0.2.0 superdsm 0.4.0 To update Imaging Image analysis Image analysis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. superdsm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 26 26 0 0 0 0 0 0 0 0 0 0 0 0 26 26 5 5
t_coffee t_coffee T-Coffee 2016-12-13 https://tcoffee.org/ 13.45.0.4846264 t-coffee 13.46.0.919e8c6b To update Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 274 311 3958 9664 1 1 1 1 0 0 0 0 0 0 0 0 9665 3959 312 275 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. 2019-04-15 1.1.0 perl-bioperl 1.7.8 To update Text Manipulation nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
treebest_best treebest_best TreeBeST best 2015-08-06 https://treesoft.sourceforge.net/treebest.shtml 1.9.2.post0 treebest 1.9.2.post1 To update Phylogenetics Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 58 966 1033 0 0 0 0 0 0 0 0 1 1 1 1 1034 967 59 46 https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09
tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal 2017-05-29 https://github.com/galaxy-genome-annotation/python-tripal python-tripal 3.2.1 To update Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
unzip unzip Unzip file 2019-08-01 https://github.com/bmcv 6.0 To update Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1765 1918 8513 9140 1 1 1 1 382 382 3072 3072 47 47 174 174 12387 11760 2348 2195 https://usegalaxy.eu/published/workflow?id=3dbee72d7c550b0c, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://workflowhub.eu/workflows/115?version=1, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1503?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 ecology/Ecoregionalization_tutorial, ecology/Obitools-metabarcoding, ecology/ecoregiolifetraits, imaging/2D-spot-detection, imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/object-tracking-using-cell-profiler, imaging/voronoi-segmentation, imaging/yolo-segmentation-training, sequence-analysis/Manage_AB1_Sanger, single-cell/scrna-ncbi-anndata
visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool 2024-09-30 https://github.com/bmcv 0.5-2 visceral-evaluatesegmentation 2021.03.25 To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation evaluatesegmentation-tool 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 10 35 0 0 0 0 0 0 0 0 0 0 0 0 35 10 2 1
voronoi_tesselation voronoi_tessellation Compute Voronoi tesselation 2024-03-09 https://github.com/bmcv 0.22.0 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 148 148 0 0 0 0 0 0 0 0 0 0 0 0 148 148 15 15 https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1 imaging/voronoi-segmentation
w4mclassfilter w4mclassfilter Filter W4M data by values or metadata 2018-08-06 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper 0.98.19 r-base To update Metabolomics eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7 10 2003 2850 0 0 0 0 4 4 1500 1905 0 0 0 0 4755 3503 14 11
w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables 2024-07-10 http://workflow4metabolomics.org 1.0.0+galaxy1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 56 56 56 56 4 4
w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results 2018-08-06 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper 0.98.18 r-base To update Metabolomics eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 13 208 382 0 0 0 0 3 3 11 11 0 0 0 0 393 219 16 15
w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets 2018-08-06 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper 0.98.2 coreutils 8.25 To update Metabolomics eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 7 132 171 0 0 0 0 0 2 0 7 0 0 0 0 178 132 9 4
wade wade identify regions of interest 2019-09-20 https://github.com/phac-nml/wade 0.2.5+galaxy1 wade 1.2.0 To update Sequence Analysis nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 4 20 58 0 0 0 0 0 0 0 0 0 0 0 0 58 20 4 1
xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw 2023-05-24 https://github.com/sneumann/xcms 4.4.0 bioconductor-xcms 4.4.0 Up-to-date Metabolomics Mass spectrum visualisation, Label-free quantification, Validation, Chromatographic alignment, Peak detection, Chromatogram visualisation, Data filtering Mass spectrum visualisation, Label-free quantification, Validation, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Data visualisation, Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 305 327 28321 44355 115 115 10237 10237 62 68 4838 6536 1306 1374 2965294 3054761 3115889 3008690 1884 1788 https://usegalaxy.eu/published/workflow?id=2179ba1c33f77f7e, https://usegalaxy.fr/published/workflow?id=06fa7dd6eea42350, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=18b2f77f2915adc7, https://usegalaxy.fr/published/workflow?id=192ff9aa79217899, https://usegalaxy.fr/published/workflow?id=19e99a5c09c01bb7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=2ee479308227a926, https://usegalaxy.fr/published/workflow?id=32f903738292a67f, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=4384e12fe70235d6, https://usegalaxy.fr/published/workflow?id=49e59327f299e9f7, https://usegalaxy.fr/published/workflow?id=4aa393a1f192a495, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5bfbe77fd6b37c45, https://usegalaxy.fr/published/workflow?id=5ec8a143f82a8c90, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7bce49f6c338905c, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=98bb6a831a2b399d, https://usegalaxy.fr/published/workflow?id=b6311795ae10032b, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=cca13353d553319e, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e3d00bdef9addd7c, https://usegalaxy.fr/published/workflow?id=e6a55d00f1364794, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org.au/published/workflow?id=f9e5caaf08a450ec, https://usegalaxy.org.au/published/workflow?id=fa0243ff9b5ca997, https://usegalaxy.org/published/workflow?id=3edd2957ecd26d6c, https://usegalaxy.org/published/workflow?id=650f3eb7647b4508, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://usegalaxy.org/published/workflow?id=b38215b4ba7a9793, https://workflowhub.eu/workflows/1582?version=1, https://workflowhub.eu/workflows/1584?version=1, https://workflowhub.eu/workflows/677?version=2, https://workflowhub.eu/workflows/680?version=2 metabolomics/gc_ms_with_xcms, metabolomics/gcms, metabolomics/lcms, metabolomics/lcms-preprocessing
10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ 2022-05-10 https://github.com/10XGenomics/bamtofastq 1.4.1 10x_bamtofastq 1.4.1 Up-to-date Convert Formats, Single Cell bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 90 90 328 328 23 23 63 63 5 5 53 53 0 0 0 0 444 444 118 118
3dtrees_tile_merge 3dtrees_tile_merge Subsampling, tiling, merging and matching of point clouds. 2025-10-14 https://github.com/3dTrees-earth/3Dtrees_Tile_Merge 1.0.1 To update Geo Science bgruening https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_tile_merge https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_tile_merge 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Wound healing scratch assay image analysis woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays 2024-02-29 https://git.embl.de/grp-cba/wound-healing-htm-screen 1.6.1 fiji-morpholibj 1.6.1 Up-to-date Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 31 31 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 https://workflowhub.eu/workflows/782?version=1
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agat agat GTF/GFF analysis toolkit 2023-05-22 https://github.com/NBISweden/AGAT 1.4.0 agat 1.5.1 To update Convert Formats, Statistics, Fasta Manipulation Data handling, Genome annotation Data handling, Genome annotation Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 516 516 7064 7064 220 220 854 854 85 85 1199 1199 17 17 228 228 9345 9345 838 838 https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://workflowhub.eu/workflows/1096?version=2
align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 To update Fasta Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1303 1347 0 0 0 0 0 0 0 0 0 0 0 0 1347 1303 42 36
antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . 2015-04-30 1.1 antarna 2.0.1.2 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 7 263 307 0 0 0 0 0 0 0 0 0 0 0 0 307 263 7 4
antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 2015-02-28 https://antismash.secondarymetabolites.org 6.1.1 antismash 8.0.4 To update Sequence Analysis Sequence clustering, Gene prediction, Differential gene expression analysis Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Molecular interactions, pathways and networks, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1083 1236 29269 32703 1017 1017 12499 12499 280 280 10622 10622 6 6 170 170 55994 52560 2539 2386 https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1558?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 genome-annotation/secondary-metabolite-discovery
aresite2 AREsite2_REST AREsite2 REST Interface 2017-02-01 http://rna.tbi.univie.ac.at/AREsite 0.1.2 python To update RNA, Data Source, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 14 36 83 0 0 0 0 0 0 0 0 0 0 0 0 83 36 14 11 https://usegalaxy.eu/published/workflow?id=4e57c5cf750afadd
atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. 2018-06-20 https://github.com/ParkerLab/atactk/ 0.1.6 atactk 0.1.9 To update Fastq Manipulation rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 60 83 148 299 0 0 0 0 0 0 0 0 0 0 0 0 299 148 83 60
bamhash bamhash Hash BAM and FASTQ files to verify data integrity 2015-09-17 https://github.com/DecodeGenetics/BamHash 1.1 bamhash 2.0 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 55 62 194 0 0 0 0 0 0 0 0 0 0 0 0 194 62 55 48
barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm 2016-06-11 https://github.com/YeoLab/gscripts 0.1.0 pysam 0.23.3 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
basecoverage gops_basecoverage_1 Base Coverage of all intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3 35 20 308 199 2294 1286 45703 22 36 321 581 1 2 3 13 46605 1630 2367 225 https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda
best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression 2014-04-01 1.0.0 numpy To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 6 4 6 8 74 14 255 0 0 0 0 0 0 0 0 261 18 80 12
bg_statistical_hypothesis_testing bg_statistical_hypothesis_testing Tool for computing statistical tests. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 74 218 415 1 1 1 1 0 0 0 0 0 0 0 0 416 219 75 53
bia_download bia_download Tool to query ftp links for study from bioimage archive 2023-12-06 https://www.ebi.ac.uk/biostudies/bioimages/studies 0.2.0 wget To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 13 13
bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format 2015-06-04 0.1.0 ucsc_tools To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 715 873 7732 9584 1 1 1 1 1 2 4 7 0 0 0 0 9592 7737 876 717
bioimage_inference bioimage_inference Load model from BioImage.IO and make inferences 2024-08-02 https://github.com/bgruening/galaxytools 2.4.1 python To update Imaging Machine learning, Computer science Machine learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. pytorch 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 9 9 133 133 0 0 0 0 1 1 68 68 0 0 0 0 201 201 10 10 https://workflowhub.eu/workflows/1526?version=1 imaging/process-image-bioimageio
biomodels biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. 2023-11-07 https://www.ebi.ac.uk/biomodels/ 1.1 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 125 125 1 1 1 1 0 0 0 0 0 0 0 0 126 126 17 17
bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data 2021-05-17 https://bionanogenomics.com/ 3.7.0 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 169 615 615 63 63 177 177 23 23 898 898 0 0 0 0 1690 1690 255 255 https://usegalaxy.eu/published/workflow?id=075c4126e66def01, https://usegalaxy.eu/published/workflow?id=2e6ed783bdf05d16, https://usegalaxy.eu/published/workflow?id=319bc351f7a8e358, https://usegalaxy.eu/published/workflow?id=3d047ed984762ce8, https://usegalaxy.eu/published/workflow?id=45c0933b5c522628, https://usegalaxy.eu/published/workflow?id=5bb7691b176d1010, https://usegalaxy.eu/published/workflow?id=bb13f30a5562d30d, https://usegalaxy.eu/published/workflow?id=f6bd10486a0ba17d, https://usegalaxy.org.au/published/workflow?id=02f2a556e77eed14, https://usegalaxy.org.au/published/workflow?id=11f1564f2bd815d8, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=53cbacc71790c41b, https://usegalaxy.org.au/published/workflow?id=73565f6cb4136370, https://usegalaxy.org.au/published/workflow?id=87bbf9408b3f2a32, https://usegalaxy.org.au/published/workflow?id=bcb0be4f4a0e369f, https://usegalaxy.org/published/workflow?id=85f521f5c7351406, https://usegalaxy.org/published/workflow?id=b1cfa3c239ef2523, https://usegalaxy.org/published/workflow?id=bff8bc8d0059274f, https://usegalaxy.org/published/workflow?id=ca3f2d9554e9e1c8, https://usegalaxy.org/published/workflow?id=d5183b025d0e78dd, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/643?version=5 assembly/vgp_genome_assembly
bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states 2015-02-28 https://www.bioinformatics.babraham.ac.uk/projects/bismark/ 0.22.1 bismark 0.25.1 To update Sequence Analysis, Next Gen Mappers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0 4 4 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 439 543 17084 20515 4 4 33 33 41 41 1423 1423 7 7 74 74 22045 18614 595 491 https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=8601a62dbca3082f
black_forest_labs_flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. 2024-10-14 https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 38 377 377 0 0 0 0 0 0 0 0 0 0 0 0 377 377 38 38
blat_coverage_report generate_coverage_report Polymorphism of the Reads 2014-05-19 1.0.0 To update Next Gen Mappers, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blat_mapping blat2wig Coverage of the Reads in wiggle format 2014-05-19 1.0.0 To update Next Gen Mappers, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. 2022-11-04 https://blobtoolkit.genomehubs.org/ 4.0.7 To update Sequence Analysis, Assembly Genome assembly, Scaffolding, Visualisation, Data deposition, Data parsing Genome assembly, Scaffolding, Visualisation Sequence assembly, Model organisms, Workflows, Phylogenomics, Zoology, Biodiversity Sequence assembly, Model organisms, Workflows, Phylogenomics, Zoology, Biodiversity bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit BlobToolKit BlobToolKit BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 148 148 3084 3084 62 62 237 237 85 85 1022 1022 1 1 2 2 4345 4345 296 296 https://usegalaxy.eu/published/workflow?id=3069c17b52decab4, https://usegalaxy.eu/published/workflow?id=88f80a31e3ff8663, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=c9a8fba4c56f5c83, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1641?version=1 assembly/ERGA-post-assembly-QC
blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. 2015-02-28 http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html 0.1.2 blockbuster 0.0.1.1 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 96 128 567 3059 15 15 20 20 11 11 368 394 0 0 0 0 3473 955 154 122 https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=b36be9100485e6cd, https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678, https://usegalaxy.eu/published/workflow?id=f00b862b06093636, https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089, https://workflowhub.eu/workflows/1671?version=1 transcriptomics/small_ncrna_clustering
blockclust blockclust BlockClust detects transcripts with similar processing patterns. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust 1.1.1 blockclust 1.1.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52 85 524 1578 40 40 132 132 15 17 704 758 0 0 0 0 2468 1360 142 107 https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678, https://usegalaxy.eu/published/workflow?id=f00b862b06093636, https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089, https://workflowhub.eu/workflows/1671?version=1 transcriptomics/small_ncrna_clustering
bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. 2012-11-26 http://bowtie-bio.sourceforge.net/ 1.2.0 bowtie 1.3.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1375 1733 22683 29140 117 17507 5706 205094 383 443 20521 20859 0 2 0 82 255175 48910 19685 1875 https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.org.au/published/workflow?id=5cf5334877cc1297, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7, https://usegalaxy.org/published/workflow?id=11dac9cba49be089, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=246da6fd63cbd49d, https://usegalaxy.org/published/workflow?id=29a80db9f3208c29, https://usegalaxy.org/published/workflow?id=31dea5361ec9421c, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3d1f4bd67ce30f99, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=486ee20613d58dcf, https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=4aad96570d252f95, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5aa2caa2dcae1477, https://usegalaxy.org/published/workflow?id=62401f33a369bac0, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=92a233e5f2405830, https://usegalaxy.org/published/workflow?id=a24092b7f00b4e2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c, https://usegalaxy.org/published/workflow?id=b0a12221ce09c001, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=b5c79535c499bc58, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6, https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f201ce61becf9a80, https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac, https://usegalaxy.org/published/workflow?id=fc09d17e0bce18f8, https://workflowhub.eu/workflows/1530?version=1 genome-annotation/tnseq
canonical_correlation_analysis cca1 Canonical Correlation Analysis 2014-05-19 1.0.0 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20 23 39 82 16 147 30 505 0 0 0 0 0 0 0 0 587 69 170 36
canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu 2.3 canu 2.3 Up-to-date Assembly De-novo assembly De-novo assembly Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1644 1843 13768 17494 0 0 0 0 454 485 3744 4325 37 37 480 480 22299 17992 2365 2135
categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. 2013-09-25 1.0.0 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 5 4 41 0 0 0 0 14 16 169 232 0 0 0 0 273 173 21 17
ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool 2014-01-27 0.0.2 ccat 3.0 To update ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27 44 61 183 0 0 0 0 0 0 0 0 0 0 0 0 183 61 44 27
cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads 2015-04-28 0.0.1 cd-hit-auxtools 4.8.1 To update Metagenomics, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 501 770 7542 9437 0 0 0 0 0 0 0 0 9437 7542 770 501 https://usegalaxy.org/published/workflow?id=35c2626849348f2c
cellpose cellpose Cellpose is an anatomical segmentation algorithm 2024-02-29 https://github.com/MouseLand/cellpose 3.1.0 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 1269 1269 0 0 0 0 3 3 216 216 0 0 0 0 1485 1485 17 17
cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper 2020-03-06 To update Imaging Quantification, Image analysis, Parsing Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype Imaging, Microarray experiment, Genotype and phenotype bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. cellprofiler 0 23 23 19 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 63 67 3870 4976 0 0 0 0 10 10 8293 8293 0 0 0 0 13269 12163 77 73 https://usegalaxy.eu/published/workflow?id=3dbee72d7c550b0c, https://workflowhub.eu/workflows/115?version=1, https://workflowhub.eu/workflows/1503?version=1, https://workflowhub.eu/workflows/1505?version=1, https://workflowhub.eu/workflows/41?version=2 imaging/object-tracking-using-cell-profiler, imaging/tutorial-CP
cellprofiler4 cp_cellprofiler4 cellProfiler4 wrapper 2021-09-15 https://github.com/CellProfiler/CellProfiler 4.2.8 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 60 60 0 0 0 0 0 0 0 0 0 0 0 0 60 60 12 12
change_case ChangeCase Convert column case. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 2560 3231 12348 15871 2179 2957 10632 19461 290 318 1023 1208 102 104 635 687 37227 24638 6610 5131 https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://workflowhub.eu/workflows/1713?version=1 transcriptomics/ref-based
chatgpt_openai_api chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. 2024-08-12 https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 59 59 612 612 0 0 0 0 0 0 0 0 0 0 0 0 612 612 59 59 https://usegalaxy.eu/published/workflow?id=a2284469005518e1
chipseeker chipseeker A tool for ChIP peak annotation and visualization 2018-05-24 https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html 1.32.0 bioconductor-chipseeker 1.42.0 To update ChIP-seq, Genome annotation rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 1169 1326 20836 25212 2625 3151 35077 40734 121 128 3595 3974 0 0 0 0 69920 59508 4605 3915 https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11
chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython 2013-09-26 0.0.3 biopython 1.70 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) 2016-06-06 https://github.com/YangLab/CIRCexplorer 1.1.9.0 circexplorer 1.1.10 To update Sequence Analysis, RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 44 132 291 0 0 0 0 7 7 341 341 0 0 0 0 632 473 51 35 https://usegalaxy.org.au/published/workflow?id=5aff01d0b5fabd84
clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio 2013-10-28 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.22.1 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cleanlab cleanlab_issue_handler CleanLab is a package to find various types of issues in a dataset. 2025-05-05 https://cleanlab.ai 2.7.1 cleanlab To update Machine Learning bgruening https://github.com/cleanlab/cleanlab https://github.com/bgruening/galaxytools/tree/master/tools/cleanlab 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins 2013-05-02 http://www.compbio.dundee.ac.uk/www-nod/ 0.1.0 clinod 1.3 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 585 585 0 0 0 0 0 0 0 0 585 585 31 31
cluster gops_cluster_1 Cluster the intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 11 37 132 894 128 1555 1898 30742 16 20 1259 1528 1 2 1 11 33175 3290 1614 156 https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=7cff5c4dadffaad5
cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. 2023-08-19 https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl 0.08+galaxy2 perl To update RNA Comparison, Alignment Comparison, Alignment Biology, Medicine Biology, Medicine rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results.This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 3102 3102 1 1 2 2 0 0 0 0 0 0 0 0 3104 3104 7 7 https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1842?version=1 microbiome/mgnify-amplicon
cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. 2017-09-22 https://github.com/eggzilla/cmv 1.0.8 cmv 1.0.8 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 8 14 19 114 0 0 0 0 0 0 0 0 0 0 0 0 114 19 14 8 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. 2015-02-28 http://www.e-rna.org/cofold/ 2.0.4.0 cofold 2.0.4 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 32 106 365 0 0 0 0 0 0 0 0 0 0 0 0 365 106 32 24
column_arrange_by_header bg_column_arrange_by_header Column arrange by header name 2015-03-02 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 486 576 7809 8379 504 504 2800 2800 98 155 1659 2063 32 32 202 202 13444 12470 1267 1120 https://usegalaxy.eu/published/workflow?id=0f7acf235096b708, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4f62794453f65cba, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=83049910e2cd5128, https://usegalaxy.eu/published/workflow?id=8f677efac7100097, https://usegalaxy.eu/published/workflow?id=930a9757252d3ca6, https://usegalaxy.eu/published/workflow?id=9a0275211e74698a, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://usegalaxy.eu/published/workflow?id=ff2fd4a4bb27d859, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://workflowhub.eu/workflows/1678?version=1, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 single-cell/bulk-deconvolution-evaluate, variant-analysis/somatic-variants
combine_metaphlan2_humann2 combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 2023-07-20 0.3.0 python To update Metagenomics Aggregation Aggregation Metagenomics, Molecular interactions, pathways and networks Metagenomics, Molecular interactions, pathways and networks bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 1972 1972 31 31 128 128 0 0 0 0 12 12 25 25 2125 2125 155 155 https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics
compalignp compalignp Compute fractional identity between trusted alignment and test alignment 2015-06-03 1.0 compalignp 1.0 Up-to-date RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 29 3 222 0 0 0 0 0 0 0 0 0 0 0 0 222 3 29 3
compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information 2022-10-19 0.2.0 To update Metagenomics Comparison Comparison Metagenomics, Gene and protein families Metagenomics, Gene and protein families bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 32 248 332 0 0 0 0 0 0 0 0 0 0 0 0 332 248 32 23
complement gops_complement_1 Complement intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12 27 20 241 154 845 422 4836 7 8 343 531 1 1 1 1 5609 786 881 174
compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. 2013-09-25 1.0.0 To update Sequence Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12 15 29 101 0 0 0 0 8 8 326 424 0 0 0 0 525 355 23 20
compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. 2013-09-25 1.0.0 To update Sequence Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 65 0 0 0 0 5 5 321 425 0 0 0 0 490 321 7 5
compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values 2014-04-01 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 35 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0
concat gops_concat_1 Concatenate two bed files 2014-04-01 https://github.com/galaxyproject/gops 1.0.1 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 705 862 578868 579385 683 3613 43922 86389 108 125 19198 19510 52 53 1321 1331 686615 643309 4653 1548 https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.eu/published/workflow?id=d52ff93f4ffdd981, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=61a21c9928182ae4, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=daff6854b5dfc6f1, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=27e1a8c651d9a298, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=5834e562fa403732, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/356?version=1 microbiome/mgnify-amplicon
condense_characters Condense characters1 Condense consecutive characters. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 371 38 2179 6 9 200 256 0 1 0 10 2445 238 381 27
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coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 42 65 955 1867 160 2124 2523 44304 13 20 294 447 1 2 4 14 46632 3776 2211 216 https://usegalaxy.eu/published/workflow?id=668a9f5da768fa30, https://usegalaxy.eu/published/workflow?id=99c4dce722c023d1, https://usegalaxy.org/published/workflow?id=08ca80ae36c8c576, https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=e6550f5289099efc
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create_tool_recommendation_model create_tool_recommendation_model Create model to recommend tools 2019-08-20 https://github.com/bgruening/galaxytools 0.0.5 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 26 86 474 33 33 74 74 0 0 0 0 0 0 0 0 548 160 59 56
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microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/clinical-mp-4-quantitation, microbiome/metaplasmidome_query, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/metaquantome-data-creation, proteomics/neoantigen-hla-binding-novel-peptides, sequence-analysis/tapscan-streptophyte-algae, single-cell/GO-enrichment, single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-seurat-pbmc3k, statistics/gpu_jupyter_lab, transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways, transcriptomics/rna-seq-viz-with-heatmap2, variant-analysis/non-dip, variant-analysis/pox-tiled-amplicon, visualisation/circos, visualisation/circos-microbial
delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5 7 13 40 0 0 0 0 0 0 0 0 0 0 0 0 40 13 7 5
dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data 2022-10-20 https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers 0.1.0+galaxy0 python To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 100 100 0 0 0 0 0 0 0 0 0 0 0 0 100 100 21 21
dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) 2013-11-28 0.1 To update Systems Biology, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 38 71 0 133 0 304 0 0 0 0 0 0 0 0 375 38 165 26
diff diff GNU diff tool that calculates the differences between two files. 2020-03-29 http://www.gnu.org/software/diffutils/ 3.10 diffutils To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 133 133 657 657 37 37 71 71 2 2 115 115 0 0 0 0 843 843 172 172 https://usegalaxy.eu/published/workflow?id=0b568c9735c03360, https://usegalaxy.eu/published/workflow?id=c917db7d7ba7ea6f, https://workflowhub.eu/workflows/1623?version=1, https://workflowhub.eu/workflows/1953?version=1 digital-humanities/introduction_to_dh, digital-humanities/text_mining_chinese
diffbind Diffbind provides functions for processing ChIP-Seq data. 2015-02-28 http://bioconductor.org/packages/release/bioc/html/DiffBind.html To update ChIP-seq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
divide_pg_snp dividePgSnp Separate pgSnp alleles into columns 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 10 13 38 17 56 41 176 0 0 0 0 0 0 0 0 214 54 66 25
dorina dorina_search data source for RNA interactions in post-transcriptional regulation 2015-05-20 1.0 To update RNA, Data Source rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 31 684 1639 0 0 0 0 0 0 0 0 0 0 0 0 1639 684 31 3
dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) 2015-06-10 5.7.a rnastructure 6.4 To update Sequence Analysis, RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence 2015-09-17 http://dotknot.csse.uwa.edu.au/ 1.3.1 vienna_rna To update RNA, Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 16 23 91 0 0 0 0 0 0 0 0 0 0 0 0 91 23 16 8
draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria 2013-09-25 1.0.0 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61 69 188 252 0 0 0 0 24 39 192 272 8 8 11 11 535 391 116 93
dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 12 176 187 0 0 0 0 187 176 12 9
dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 8 164 170 0 0 0 0 170 164 8 7
dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 7 161 168 0 0 0 0 168 161 7 5
dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 8 170 177 0 0 0 0 177 170 8 7
dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms 2014-01-27 1.0.2 r-bitops To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 4 2 36 4 4 11 11 5 7 207 265 2 2 2 2 314 222 17 12
edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 2022-10-16 https://github.com/oushujun/EDTA edta 2.2.2 To update Variant Analysis De-novo assembly, Deisotoping, Genome annotation De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 164 164 4750 4750 0 0 0 0 0 0 0 0 0 0 0 0 4750 4750 164 164
effectivet3 effectiveT3 Find bacterial type III effectors in protein sequences 2013-04-30 http://effectors.org 0.0.21 effectiveT3 1.0.1 To update Sequence Analysis Sequence classification Sequence classification Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. 2018-03-02 https://github.com/lamortenera/epicseg @VERSION_STRING@ epicseg 1.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 22 86 257 0 0 0 0 0 0 0 0 0 0 0 0 257 86 22 16
erga_ear make_ear A tool to compile assembly reports and stastics from assembly pipeline 2024-06-07 https://github.com/ERGA-consortium/EARs/tree/main 24.10.15 reportlab To update Sequence Analysis, Assembly bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 99 99 0 0 0 0 0 0 0 0 0 0 0 0 99 99 4 4
exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. 2015-02-28 http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp 1.0.1 exparna 1.0.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
express express Quantify the abundances of a set of target sequences from sampled subsequences 2014-01-27 1.1.1 eXpress 1.5.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34 51 235 372 0 117 0 1184 21 61 2444 2995 0 0 0 0 4551 2679 229 55
fasta_compute_length fasta_compute_length Compute sequence length 2014-05-19 https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.4 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1172 1456 10749 12600 1571 6133 19547 54934 189 236 5789 6166 21 22 332 342 74042 36417 7847 2953 https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=2f053b615d9788bf, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=a31100610fba17a1, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=ada52ba09b462567, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e, https://usegalaxy.eu/published/workflow?id=c696b37d1bf68e9b, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=5cfea39918e8632d, https://usegalaxy.org.au/published/workflow?id=6b1b0a945d367b4c, https://usegalaxy.org.au/published/workflow?id=b432a1312859edd2, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=3a92253f57e553bd, https://usegalaxy.org/published/workflow?id=400c1d170f073279, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=8e1c6ad6ff623015, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=c88fe3dc11bc4905, https://usegalaxy.org/published/workflow?id=cdf5dffbed938d49, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1632?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/439?version=4, https://workflowhub.eu/workflows/625?version=27, https://workflowhub.eu/workflows/880?version=1 assembly/ecoli_comparison, sequence-analysis/viral_primer_design, single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-standard-processing-snapatac2, variant-analysis/pox-tiled-amplicon
fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species 2014-05-19 0.0.1 bx-python 0.14.0 To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 332 39190 42990 580 1506 21098 27311 97 129 1927 2787 6 8 323 344 73432 62538 1975 959 https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4
fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) 2017-02-02 https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta_filter_by_length fasta_filter_by_length Filter sequences by length 2014-05-19 1.2 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1122 1339 55587 76393 1415 4026 50212 106640 289 358 3630 6298 26 27 437 447 189778 109866 5750 2852 https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=927b8f90ad9603a7, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=de9c2db125a5ea27, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/645?version=14 assembly/assembly-with-preprocessing, assembly/ecoli_comparison
fasta_to_tabular fasta2tab FASTA-to-Tabular converter 2014-05-19 1.1.1 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1996 2390 117300 135717 2227 9101 56007 198933 343 435 5795 8617 40 45 931 959 344226 180033 11971 4606 https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, 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fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) 2017-02-02 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_info fastq_info FASTQ info allows to validate single or paired fastq files 2021-09-12 https://github.com/nunofonseca/fastq_utils 0.25.1 fastq_utils 0.25.3 To update Fastq Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1769 1769 17127 17127 2373 2373 10656 10656 0 0 0 0 0 0 0 0 27783 27783 4142 4142 https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
fastq_pair_names fastq_pair_names Extract FASTQ paired read names 2014-05-05 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 To update Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window 2014-01-27 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 984 1208 5036 7413 2977 11843 25265 102069 237 393 2092 3355 112 112 309 309 113146 32702 13556 4310 https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=8d47811c6154d347, https://usegalaxy.org.au/published/workflow?id=9176f8ebac92d10c, https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3, https://usegalaxy.org/published/workflow?id=1cd08f3549cf5589, https://usegalaxy.org/published/workflow?id=1d1ee1fad4e20eeb, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3fbaa9ae67362495, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=7253824f78a90431, https://usegalaxy.org/published/workflow?id=73d98e5f821a78b3, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71
fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data 2014-05-19 1.0.0 To update Convert Formats, Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 8 0 0 0 0 0 0 0 0 8 0 3 0
featurecounter featureCoverage1 Feature coverage 2014-04-01 2.0.0 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 23 22243 22395 51 354 202 13720 0 0 0 0 0 0 0 0 36115 22445 377 69 https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045, https://usegalaxy.org/published/workflow?id=66748e20a243eafe
ffmpeg ffmpeg_converter A complete, cross-platform solution to record, convert and stream audio and video. 2025-04-21 https://ffmpeg.org 0.1.0 ffmpeg To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/ffmpeg https://github.com/bgruening/galaxytools/tree/master/tools/ffmpeg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts 2014-01-27 0.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 11 22 25 17 243 47 643 2 2 2 2 0 0 0 0 670 71 256 28
find_diag_hits find_diag_hits Find diagnostic hits 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 13 26 71 1 204 3 1787 0 0 0 0 0 0 0 0 1858 29 217 10
find_subsequences bg_find_subsequences 2015-03-19 0.3 biopython 1.70 To update bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 64 87 884 1408 260 409 2621 3777 3 3 264 264 0 0 0 0 5449 3769 499 327 https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.eu/published/workflow?id=b86f3775aa1f13bc, https://workflowhub.eu/workflows/1530?version=1 genome-annotation/tnseq
flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval 2014-04-01 https://github.com/galaxyproject/gops 4.0.1 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52 70 466 844 232 2573 1669 33003 18 26 1282 1664 2 3 14 24 35535 3431 2672 304 https://usegalaxy.org/published/workflow?id=6471aa8abbb3fa40, https://usegalaxy.org/published/workflow?id=7bc71a005c6f18d0
flexynesis flexynesis, flexynesis_cbioportal_import, flexynesis_plot, flexynesis_utils This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. 2024-08-12 https://github.com/BIMSBbioinfo/flexynesis/tree/main 1.1.3 flexynesis 1.1.3 Up-to-date Machine Learning, Statistics, Systems Biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 303 303 0 0 0 0 0 0 0 0 0 0 0 0 303 303 5 5 https://workflowhub.eu/workflows/1849?version=1, https://workflowhub.eu/workflows/1852?version=1, https://workflowhub.eu/workflows/1873?version=1, https://workflowhub.eu/workflows/1874?version=1 statistics/flexynesis_cbio_import, statistics/flexynesis_classification, statistics/flexynesis_survival, statistics/flexynesis_unsupervised
flye flye Assembly of long and error-prone reads. 2018-09-22 https://github.com/fenderglass/Flye/ 2.9.6 flye 2.9.6 Up-to-date Assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Sequence assembly, Metagenomics, Whole genome sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. 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footprint footprint Find transcription factor footprints 2017-04-18 https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ 1.0.0 footprint 1.0.1 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 5 56 57 0 0 0 0 0 0 0 0 0 0 0 0 57 56 5 4
format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 2022-10-19 1.0.0+galaxy1 To update Fasta Manipulation bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 78 228 287 0 0 0 0 0 0 0 0 0 0 0 0 287 228 78 68
format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels 2022-10-19 0.2.0 To update Metagenomics Formatting Formatting Taxonomy, Metagenomics Taxonomy, Metagenomics bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 555 731 6485 7678 0 0 0 0 0 0 0 0 0 0 0 0 7678 6485 731 555 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b
generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA 2014-07-28 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 94 151 95 274 434 1071 14 17 186 244 2 2 2 2 1468 716 329 141
get_flanks get_flanks1 Get flanks returns flanking region/s for every gene 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 2463 4589 326514 2009 6814 8393 243076 102 156 742 1198 10 11 14 24 570812 13738 9444 3756 https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6, https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73, https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66, https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab, https://usegalaxy.org/published/workflow?id=888bfce1c214ab64, https://usegalaxy.org/published/workflow?id=8a3e457a9453c313, https://usegalaxy.org/published/workflow?id=94de815260acc3a8, https://usegalaxy.org/published/workflow?id=c2b299627d2baf48, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://workflowhub.eu/workflows/1478?version=1 introduction/galaxy-intro-peaks2genes
get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 268 268 1372 1372 0 0 0 0 312 312 2219 2219 8 10 65 72 3663 3656 590 588 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=a1518a029132ee3d, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f, https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891
getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments 2014-04-01 1.0.0 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 88 30 296 0 0 0 0 0 0 0 0 296 30 88 16
getindels_2way getIndels_2way Fetch Indels from pairwise alignments 2014-04-01 1.0.0 numpy To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 61 27 237 0 0 0 0 0 0 0 0 237 27 61 21
gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. 2022-03-08 https://github.com/vgl-hub/gfastats 1.3.11 gfastats 1.3.11 Up-to-date Sequence Analysis Data handling Data handling Computational biology Computational biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1105 1105 19582 19582 735 735 15352 15352 183 183 4128 4128 5 5 453 453 39515 39515 2028 2028 https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=012762cb4acb068b, https://usegalaxy.eu/published/workflow?id=01fe4c590e608103, 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gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.1.1 taxonomy 0.10.1 To update Metagenomics Database search, ID mapping Database search, ID mapping Taxonomy Taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 68 116 244 713 17 1798 113 14058 0 0 0 0 0 1 0 6 14777 357 1915 85 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) 2015-02-28 https://ccb.jhu.edu/software/glimmerhmm/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gmaj gmaj_1 GMAJ Multiple Alignment Viewer 2014-01-27 2.0.1 To update Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 7 12 12 22 230 67 985 5 8 8 11 1 1 1 1 1009 88 246 35
gotohscan rbc_gotohscan Find subsequences in db 2015-07-02 1.3.0 gotohscan 2.0 To update Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 8 6 73 0 0 0 0 0 0 0 0 0 0 0 0 73 6 8 5
graph_converter graph_converter Convert between different graph formats 2015-02-28 0.1.0 To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. 2015-02-28 http://www.bioinf.uni-freiburg.de/Software/GraphClust/ 0.1 GraphClust To update RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0
graphclust_aggregate_alignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. 2018-10-24 0.6.0 graphclust-wrappers 0.6.0 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13 17 17 120 0 0 0 0 0 0 0 0 0 0 0 0 120 17 17 13
graphclust_align_cluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. 2018-10-22 0.1 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 27 31 91 3113 0 0 0 0 0 0 0 0 0 0 0 0 3113 91 31 27
graphclust_cmfinder cmFinder Determines consensus motives for sequences. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 68 24130 57259 0 0 0 0 0 0 0 0 0 0 0 0 57259 24130 68 44 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_fasta_to_gspan gspan Second step of GraphClust 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 28 66 164 0 0 0 0 0 0 0 0 0 0 0 0 164 66 28 19
graphclust_mlocarna locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 68 24174 57392 0 0 0 0 0 0 0 0 0 0 0 0 57392 24174 68 43 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_motif_finder_plot motifFinderPlot Plotting results for GraphClust 2017-02-22 0.4 seaborn To update RNA rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7 10 13 71 0 0 0 0 0 0 0 0 0 0 0 0 71 13 10 7
graphclust_nspdk NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. 2016-12-15 9.2.3.1 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 47 75 2223 63256 0 0 0 0 0 0 0 0 0 0 0 0 63256 2223 75 47 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_postprocessing glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. 2016-12-15 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 73 725 2236 0 0 0 0 0 0 0 0 0 0 0 0 2236 725 73 48 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_postprocessing_no_align graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. 2018-10-25 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 3 0 108 0 0 0 0 0 0 0 0 0 0 0 0 108 0 3 0
graphclust_prepocessing_for_mlocarna preMloc This tool prepares files for locarna step. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 74 798 2247 0 0 0 0 0 0 0 0 0 0 0 0 2247 798 74 48 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphclust_preprocessing preproc Preprocessing input for GraphClust 2016-12-15 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 56 84 733 2026 0 0 0 0 0 0 0 0 0 0 0 0 2026 733 84 56 https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick 2016-12-26 http://www.graphicsmagick.org 1.3.45 graphicsmagick 1.3.26 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 75 88 2336 3749 10 10 94 94 0 0 0 0 0 0 0 0 3843 2430 98 85 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1745?version=2, https://workflowhub.eu/workflows/1840?version=1, https://workflowhub.eu/workflows/1848?version=1, https://workflowhub.eu/workflows/807?version=1 climate/pangeo, ecology/x-array-map-plot, galaxy-interface/workflow-posters, imaging/electrophoresis-gel-bands-image-analysis, imaging/yolo-segmentation-training
graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. 2018-09-27 https://github.com/isovic/graphmap/ 0.5.2 graphmap 0.6.4 To update Assembly Sequence trimming, EST assembly, Read mapping Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing Gene transcripts, RNA-Seq, RNA splicing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 325 372 6375 7914 0 0 0 0 0 0 0 0 5 5 8 8 7922 6383 377 330
graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. 2018-05-24 https://github.com/dmaticzka/GraphProt 1.1.7+galaxy2 graphprot 1.1.7 To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 24 181 504 0 0 0 0 0 0 0 0 0 0 0 0 504 181 24 20 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf
hclust2 hclust2 Plots heatmaps 2018-07-22 https://bitbucket.org/nsegata/hclust2/ 0.99 hclust2 1.0.0 To update Data Visualization rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hgv_fundo hgv_funDo FunDO human genes associated with disease terms 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 19 397 55 1794 0 0 0 0 0 0 0 0 1794 55 397 19
hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve 2013-09-25 https://www.ebi.ac.uk/huber-srv/hilbert/ 1.0.0 R To update Graphics, Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 12 60 110 265 0 0 0 0 0 0 0 0 265 110 60 12
hictk hictk Convert cooler to juicebox_hic 2024-02-03 https://github.com/paulsengroup/hictk 2.0.2 hictk 2.1.5 To update Convert Formats, Epigenetics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 160 160 0 0 0 0 0 0 0 0 0 0 0 0 160 160 28 28
hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. 2017-03-09 https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html 0.9.2 To update Epigenetics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 39 47 782 1243 38 38 766 766 0 0 0 0 0 0 0 0 2009 1548 85 77 https://usegalaxy.eu/published/workflow?id=57b96a59cca0e8df, https://usegalaxy.eu/published/workflow?id=7d49f41cd294e15b, https://usegalaxy.eu/published/workflow?id=83fea2e4508bc3ed, https://usegalaxy.eu/published/workflow?id=cbe9e09ed3e91e2e, https://usegalaxy.org/published/workflow?id=2ffae50d0916b641, https://usegalaxy.org/published/workflow?id=43cea919ebf9d978, https://usegalaxy.org/published/workflow?id=748c1a9d85eb61e2, https://usegalaxy.org/published/workflow?id=ba4815ec62edab04
hisat hisat HISAT is a fast and sensitive spliced alignment program. 2015-05-13 http://ccb.jhu.edu/software/hisat/index.shtml 1.0.3 hisat To update Assembly devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 228 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0
histogram histogram_rpy Histogram of a numeric column 2014-07-28 https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 1.0.5 rpy2 2.7.8 To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 971 1233 4048 5378 1552 7484 6094 49673 218 372 712 1126 188 190 482 590 56767 11336 9279 2929 https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a2b386eef5645acd, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=13a550ed56b56502, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=25adc55d2a26e34b, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6, https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1458?version=1, https://workflowhub.eu/workflows/1462?version=1, https://workflowhub.eu/workflows/1469?version=1 microbiome/metaplasmidome_query, proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/protein-quant-sil
homer Software for motif discovery and next generation sequencing analysis. 2015-02-28 http://homer.salk.edu/homer/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
htseq_clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets 2022-10-11 https://github.com/EMBL-Hentze-group/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 27 27 146 146 0 0 0 0 0 0 0 0 0 0 0 0 146 146 27 27
illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. 2015-05-05 http://fiji.sc 20240614 To update Imaging Image analysis, Image annotation, Visualisation Image analysis, Image annotation, Visualisation Imaging Imaging imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 imagej ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. imagej2 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 12 13 515 1918 0 0 0 0 0 0 0 0 0 0 0 0 1918 515 13 12 https://workflowhub.eu/workflows/1259?version=1
imagemagick imagemagick_image_compare, imagemagick_image_convert, imagemagick_image_montage Contains tools based on ImageMagick 2025-08-29 https://imagemagick.org/ 7.1.2-2 imagemagick To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagemagick https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagemagick 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://usegalaxy.org/published/workflow?id=3a92253f57e553bd, https://usegalaxy.org/published/workflow?id=67252039bce060b2, https://usegalaxy.org/published/workflow?id=beefb67de2b0728c, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://workflowhub.eu/workflows/625?version=27, https://workflowhub.eu/workflows/632?version=12
indels_3way indels_3way Fetch Indels from 3-way alignments 2013-09-25 1.0.3 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 22 2 21 3 292 0 0 0 0 0 0 0 0 314 3 22 2
infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. 2015-02-28 http://infernal.janelia.org/ 1.1.5 infernal 1.1.5 Up-to-date RNA Nucleic acid feature detection Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics Sequence sites, features and motifs, Structural genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal infernal Infernal Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 103 149 57566 128051 2 2 8 8 10 10 1244 1548 0 0 0 0 129607 58818 161 115 https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1, https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1842?version=1 microbiome/mgnify-amplicon
inforna inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. 2015-02-28 http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp 2.1.2 inforna 2.1.2 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
instagraal instagraal Large genome reassembly based on Hi-C data 2022-11-10 https://github.com/koszullab/instaGRAAL 0.1.6 To update Assembly Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 16 16 160 160 0 0 0 0 0 0 0 0 0 0 0 0 160 160 16 16
intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. 2017-02-09 https://github.com/BackofenLab/IntaRNA 3.4.1 intarna 3.4.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 55 223683 228312 0 0 0 0 0 0 0 0 0 0 0 0 228312 223683 55 44
intersect gops_intersect_1 Intersect the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2552 3495 19923 352369 4361 14841 49357 791098 578 687 6876 8443 110 112 744 764 1152674 76900 19135 7601 https://usegalaxy.eu/published/workflow?id=013cc98f55b01d5d, https://usegalaxy.eu/published/workflow?id=0edf0e9a778cb732, https://usegalaxy.eu/published/workflow?id=124f884ee53685e8, https://usegalaxy.eu/published/workflow?id=13a7b30df801ea47, https://usegalaxy.eu/published/workflow?id=24ef0d03f58d4fc5, https://usegalaxy.eu/published/workflow?id=4309cbf427fa1f78, https://usegalaxy.eu/published/workflow?id=4516fe237a7112cc, https://usegalaxy.eu/published/workflow?id=68f7300f922f548d, https://usegalaxy.eu/published/workflow?id=69eed719f9b5b99d, https://usegalaxy.eu/published/workflow?id=6a48604ef9ceb8b8, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=937fa7f2f83bb735, https://usegalaxy.eu/published/workflow?id=941bc727b61c09ab, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=ad636a8e1763580a, https://usegalaxy.eu/published/workflow?id=af7926dfd0f3501c, https://usegalaxy.eu/published/workflow?id=c4cefff5b812aae9, https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6, https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73, https://usegalaxy.org.au/published/workflow?id=5668c42a05ca6be4, https://usegalaxy.org.au/published/workflow?id=a9e52a40b63d26fc, https://usegalaxy.org.au/published/workflow?id=b0b8b8f79b467cf6, https://usegalaxy.org.au/published/workflow?id=f27f6ed478d7a258, https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66, https://usegalaxy.org/published/workflow?id=165af757a6b84be9, https://usegalaxy.org/published/workflow?id=27e1a8c651d9a298, https://usegalaxy.org/published/workflow?id=30507545aa971637, https://usegalaxy.org/published/workflow?id=37383240151a472a, https://usegalaxy.org/published/workflow?id=4375f00f8a285088, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=60b080dc16141121, https://usegalaxy.org/published/workflow?id=7942748c29d718f8, https://usegalaxy.org/published/workflow?id=888bfce1c214ab64, https://usegalaxy.org/published/workflow?id=8e5efd04399c6838, https://usegalaxy.org/published/workflow?id=8e9882d890ee5ec7, https://usegalaxy.org/published/workflow?id=9005ecd577bd9bfa, https://usegalaxy.org/published/workflow?id=9238f7208033d0d6, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=b1cd3f793187d667, https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d, https://usegalaxy.org/published/workflow?id=c2b299627d2baf48, https://usegalaxy.org/published/workflow?id=dd949127e22f9f1f, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda, https://usegalaxy.org/published/workflow?id=e4f6b68301aafd38, https://usegalaxy.org/published/workflow?id=e81a10ac8b20c801, https://usegalaxy.org/published/workflow?id=ebac500f62f4a469, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://usegalaxy.org/published/workflow?id=f637ea9a753cfbe8, https://workflowhub.eu/workflows/1475?version=1, https://workflowhub.eu/workflows/1478?version=1, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1544?version=1 genome-annotation/gene-centric, introduction/galaxy-intro-peaks2genes, introduction/galaxy-intro-strands
iprscan5 Interproscan queries the interpro database and provides annotations. 2015-02-28 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. 2022-05-02 https://microbiology.se/software/itsx/ 1.1.3 itsx 1.1.3 Up-to-date Metagenomics Sequence feature detection Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Functional, regulatory and non-coding RNA, Microbiology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 140 140 2878 2878 0 0 0 0 18 18 198 198 0 0 0 0 3076 3076 158 158 https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67
jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool 2024-06-04 https://jbrowse.org 2.17.0 jbrowse2 3.6.5 To update Sequence Analysis Genome visualisation, Structure visualisation, Pathway visualisation Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Mapping, Structural variation, Genomics, Gene structure, Sequence assembly fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 626 626 3765 3765 349 349 1248 1248 95 95 603 603 0 0 0 0 5616 5616 1070 1070 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=84414f3441946702, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=ce8bf03d3df24806, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050 epigenetics/formation_of_super-structures_on_xi
join gops_join_1 Join the intervals of two datasets side-by-side 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1323 2559 14041 332406 6315 39946 37461 517154 149 303 942 1764 34 35 216 226 851550 52660 42843 7821 https://usegalaxy.eu/published/workflow?id=04b838103aed1929, https://usegalaxy.eu/published/workflow?id=29346872085adf1f, https://usegalaxy.eu/published/workflow?id=2f7149d02db43b7b, https://usegalaxy.eu/published/workflow?id=3e91f8417a66d02c, https://usegalaxy.eu/published/workflow?id=4a33a8348ac03f00, https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822, https://usegalaxy.eu/published/workflow?id=579a56c129883cf3, 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join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. 2017-11-26 1.0.1 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 354 498 1870 2985 0 0 0 0 56 66 1383 1538 7 7 17 17 4540 3270 571 417 https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.eu/published/workflow?id=e573c6b697524e3a, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://workflowhub.eu/workflows/1587?version=1 metabolomics/msi-finding-nglycans
kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis 2014-05-19 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 5 5 71 36 84 152 364 0 0 0 0 0 0 0 0 435 157 89 40
kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis 2014-05-19 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24 33 99 160 84 259 225 728 0 0 0 0 4 4 7 7 895 331 296 112
kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. 2015-02-28 http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. 2015-08-05 https://bitbucket.org/natefoo/taxonomy 1.2+galaxy0 gawk To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1365 1376 33158 33186 1892 2555 18299 28718 564 576 19721 19871 0 0 0 0 81775 71178 4507 3821 https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=a459c311f461adce, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=bd4e3cdc7f29049b, https://usegalaxy.eu/published/workflow?id=ca80039c4933aa0a, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=ee0005a5487653ba, https://usegalaxy.org/published/workflow?id=a63927dd19759714, https://usegalaxy.org/published/workflow?id=b68ec42db8953569, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/101?version=1, https://workflowhub.eu/workflows/124?version=1
labels bg_labels remaps and annotates alignments 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads 2012-11-26 1.1.1 lastz 1.04.52 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 4 2 9 0 0 0 0 3 5 5 10 0 0 0 0 19 7 9 5
lca_wrapper lca1 Find lowest diagnostic rank 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.1 taxonomy 0.10.1 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 20 11 137 14 1112 112 6136 0 0 0 0 0 0 0 0 6273 123 1132 17 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
lda_analysis lda_analy1 Perform Linear Discriminant Analysis 2014-07-28 1.0.1 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46 57 125 178 95 336 780 1639 0 3 0 4 5 5 19 19 1840 924 401 146
lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data 2016-06-04 https://github.com/mourisl/Lighter 1.0 lighter 1.1.3 To update Sequence Analysis, Fasta Manipulation k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics Whole genome sequencing, DNA, Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 31 37 106 196 0 0 0 0 0 0 0 0 0 0 0 0 196 106 37 31
linear_regression LinearRegression1 Perform Linear Regression 2014-04-01 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 282 102 1146 0 0 0 0 0 0 0 0 1146 102 282 31 https://usegalaxy.org/published/workflow?id=857db984ff571191
llm_hub llm_hub LiteLLM - Call all LLM APIs using the OpenAI format. 2025-08-20 https://github.com/bgruening/galaxytools/tree/master/tools/llm_hub 1.101.0 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/llm_hub https://github.com/bgruening/galaxytools/tree/master/tools/llm_hub 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 37 37 0 0 0 0 0 0 0 0 0 0 0 0 37 37 8 8 https://usegalaxy.eu/published/workflow?id=87546e050916dd0e
locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs 2015-02-28 http://www.bioinf.uni-freiburg.de/Software/LocARNA/ 2.0.1 locarna 2.0.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 50 318 370 0 0 0 0 0 0 0 0 0 0 0 0 370 318 50 33 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73
logistic_regression_vif LogisticRegression Perform Logistic Regression with vif 2014-04-01 1.0.1 numpy To update Sequence Analysis, Variant Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 48 23 173 0 0 0 0 0 0 0 0 173 23 48 10
maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file 2014-04-01 1.0.0 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 28 9 356 0 0 0 0 0 0 0 0 356 9 28 5
mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences 2015-06-16 https://mafft.cbrc.jp/alignment/software/ 7.526 mafft 7.525 To update RNA Multiple sequence alignment Multiple sequence alignment Sequence analysis Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 2844 3060 164403 217226 4659 6641 99571 145229 1279 1462 23332 25716 158 160 5367 5382 393553 292673 11323 8940 https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=941400d10c346b2c, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=d102a20c31d4673c, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=b3974acb70608e38, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef, https://usegalaxy.org/published/workflow?id=956987e628530c79, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=f737593a1db217c8, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1627?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1839?version=1 evolution/abc_intro_phylo, genome-annotation/gene-centric, sequence-analysis/tapscan-streptophyte-algae, sequence-analysis/viral_primer_design, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon
mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track 2014-05-19 1.0.0 To update Visualization, Convert Formats, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
markitdown markitdown Convert documents to Markdown using markitdown 2025-04-21 https://github.com/microsoft/markitdown 0.1.3 python To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/markitdown https://github.com/bgruening/galaxytools/tree/master/tools/markitdown 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 51 51 0 0 0 0 0 0 0 0 0 0 0 0 51 51 8 8
mavedb_importer mavedb_importer data source for MaveDB 2023-12-13 0.9 To update Data Source bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2
mea mea Maximum expected accuracy prediction 2015-07-29 http://www.bioinf.uni-leipzig.de/Software/mea 0.6.4.1 mea 0.6.4 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 5 9 86 0 0 0 0 0 0 0 0 0 0 0 0 86 9 5 3
megablast_xml_parser megablast_xml_parser Parse blast XML output 2014-05-19 1.0.1 python To update Next Gen Mappers, Convert Formats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 98 152 1457 1614 88 477 258 2907 0 0 0 0 0 0 0 0 4521 1715 629 186 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a
merge gops_merge_1 Merge the overlapping intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 432 482 567865 568928 561 4421 45860 108947 93 139 19554 20122 9 10 1171 1181 699178 634450 5052 1095 https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.eu/published/workflow?id=d52ff93f4ffdd981, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=61a21c9928182ae4, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=5834e562fa403732, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/356?version=1
merge_cols mergeCols1 Merge columns together. 2012-12-04 1.0.3 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 2264 2636 27989 40501 841 3343 19933 135060 101 167 1612 2136 115 116 616 626 178323 50150 6262 3321 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=57cfe5062c8e01bf, https://usegalaxy.eu/published/workflow?id=5e09d5e991009cda, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=d0ae255151450dad, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=138311394c077827, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=2d64e09025ae8ed4, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=5bc973dd30f22525, https://usegalaxy.org/published/workflow?id=66748e20a243eafe, https://usegalaxy.org/published/workflow?id=68a9f03d99676bdc, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8b1eedebcb94ba93, https://usegalaxy.org/published/workflow?id=941ced9f12eecd3c, https://usegalaxy.org/published/workflow?id=9864961cc6132562, https://usegalaxy.org/published/workflow?id=b8742810ac30429d, https://usegalaxy.org/published/workflow?id=c17fa637bcdec86e, https://usegalaxy.org/published/workflow?id=c3ea8fa3bb202dc6, https://usegalaxy.org/published/workflow?id=cd1badac800122c2, https://usegalaxy.org/published/workflow?id=e3e646407e3f921d, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/1680?version=1, https://workflowhub.eu/workflows/1696?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/1704?version=1 assembly/ecoli_comparison, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/regionalGAM, transcriptomics/rna-seq-counts-to-genes
methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 124 423 5461 0 0 0 0 0 0 0 0 0 0 0 0 5461 423 124 31
methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. 2016-12-20 http://bioconductor.org/packages/release/bioc/html/methylKit.html 0.99.2 bioconductor-methylkit 1.32.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 10 10 10 10 3 3
metilene metilene Differential DNA methylation calling 2015-12-14 0.2.6.1 metilene 0.2.8 To update RNA, Statistics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 285 505 3013 5261 148 148 786 786 57 57 450 452 1 1 1 1 6500 4250 711 491 https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee, https://workflowhub.eu/workflows/1566?version=1 epigenetics/methylation-seq
mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. 2024-05-14 https://github.com/jstjohn/SeqPrep 1.2 To update Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 1348 1348 109 109 444 444 0 0 0 0 0 0 0 0 1792 1792 115 115 https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 microbiome/mgnify-amplicon
miclip mi_clip Identification of binding sites in CLIP-Seq data. 2015-02-28 https://cran.r-project.org/src/contrib/Archive/MiClip/ 1.2.0 Rscript To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments 2014-04-01 1.0.0 sputnik To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 147 98 987 0 0 0 0 0 0 0 0 987 98 147 50
microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes 2014-04-01 1.1.0 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 91 36 318 0 0 0 0 0 0 0 0 318 36 91 24
minced minced MinCED - Mining CRISPRs in Environmental Datasets 2015-02-28 http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README 0.2.0 minced 0.4.2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 169 8010 8360 0 0 0 0 0 0 0 0 0 0 0 0 8360 8010 169 152
mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration 2014-07-28 0.0.1 MINE To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 7 12 7 22 20 68 0 0 0 0 0 0 0 0 80 27 31 14
minipolish minipolish Polishing miniasm assemblies 2022-10-19 https://github.com/rrwick/Minipolish 0.2.0 minipolish 0.2.0 Up-to-date Sequence Analysis Localised reassembly, Read depth analysis Localised reassembly, Read depth analysis Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 278 278 0 0 0 0 0 0 0 0 0 0 0 0 278 278 43 43
mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. 2021-05-29 https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 3.2.3 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 265 265 1632 1632 177 177 1198 1198 45 45 983 983 0 0 0 0 3813 3813 487 487 https://usegalaxy.eu/published/workflow?id=2062c7e1c50b05f3, https://usegalaxy.eu/published/workflow?id=32a0c4bbe6f9add9, https://usegalaxy.eu/published/workflow?id=c0c8228673b7191f, https://usegalaxy.eu/published/workflow?id=e71ae1076d5f0584, https://usegalaxy.org.au/published/workflow?id=2f49a0a03d99c57a, https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf, https://usegalaxy.org.au/published/workflow?id=8004dce1906ec057, https://usegalaxy.org.au/published/workflow?id=fc74419b109527b2, https://usegalaxy.org/published/workflow?id=40be58638e230ab5, https://usegalaxy.org/published/workflow?id=5f621330d6339655, https://usegalaxy.org/published/workflow?id=67b9046dc5dbc009, https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae, https://workflowhub.eu/workflows/1648?version=1, https://workflowhub.eu/workflows/738?version=4 assembly/mitochondrion-assembly
molecule_to_gspan bg_mol2gspan converter 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. 2024-09-06 https://github.com/motu-tool/mOTUs 3.1.0 motus 3.1.0 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 377 377 0 0 0 0 0 0 0 0 0 0 0 0 377 377 40 40
mqc mqc Ribosome profiling mapping quality control tool 2017-08-11 https://github.com/Biobix/mQC 1.9 mqc 1.10 To update Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 11 45 81 0 0 0 0 0 0 0 0 0 0 0 0 81 45 11 8
multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites 2013-09-25 1.0.0 bx-sputnik To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot 2014-05-22 http://mummer.sourceforge.net/ 0.0.8 ghostscript 9.18 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 265 299 1105 1224 308 308 1031 1031 15 49 48 202 1 1 3 3 2460 2187 657 589
music music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) 2021-09-12 https://github.com/xuranw/MuSiC 0.1.1 music-deconvolution 0.1.1 Up-to-date Transcriptomics, Single Cell bgruening https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution music_deconvolution MuSiC Deconvolution MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 117 117 4406 4406 57 57 652 652 11 11 2332 2332 0 0 0 0 7390 7390 185 185 https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=39dd6365ff076dc4, https://usegalaxy.eu/published/workflow?id=cb978151b1686b71, https://usegalaxy.eu/published/workflow?id=d1ab8eabcbe0a004, https://workflowhub.eu/workflows/1498?version=1, https://workflowhub.eu/workflows/1542?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1553?version=1, https://workflowhub.eu/workflows/1557?version=1, https://workflowhub.eu/workflows/1575?version=1 single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/bulk-music-4-compare
mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs 2013-09-25 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 5 8 49 16 122 27 424 0 0 0 0 0 0 0 0 473 35 127 20 https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4
nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. 2018-05-28 https://github.com/jts/nanopolish 0.14.0 nanopolish 0.14.0 Up-to-date bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 88 108 8229 9899 0 0 0 0 16 17 2510 3015 4 4 75 75 12989 10814 129 108 https://usegalaxy.eu/published/workflow?id=1cc3b4f1b50ba427, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d, https://usegalaxy.eu/published/workflow?id=816815a93cc68244, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://workflowhub.eu/workflows/50?version=1, https://workflowhub.eu/workflows/51?version=1
nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq 2017-02-21 https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ 1.0 r-nastiseq 1.0 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 2 42 0 0 0 0 0 0 0 0 0 0 0 0 42 2 2 1
netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis 2022-08-24 1.6.0 bioconductor-netboxr 1.9.0 To update Systems Biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 28 28 0 0 0 0 0 0 0 0 0 0 0 0 28 28 11 11
nextdenovo nextdenovo String graph-based de novo assembler for long reads 2023-02-09 https://github.com/Nextomics/NextDenovo 2.5.0 nextdenovo 2.5.2 To update Assembly De-novo assembly, Genome assembly De-novo assembly, Genome assembly Sequencing, Sequence assembly Sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo nextdenovo NextDenovo NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 252 252 703 703 111 111 265 265 0 0 0 0 0 0 0 0 968 968 363 363 https://workflowhub.eu/workflows/789?version=1
nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences 2013-04-17 http://www.moseslab.csb.utoronto.ca/NLStradamus 0.0.11 NLStradamus 1.8 To update Fasta Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome 2016-09-27 https://genie.weizmann.ac.il/software/nucleo_exe.html 3.0 nucleosome_prediction 3.0 Up-to-date Sequence Analysis Prediction and recognition, Nucleosome position prediction, Sequence analysis Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Structural genomics, Nucleic acid sites, features and motifs bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 27 20 866 0 0 0 0 0 0 0 0 0 0 0 0 866 20 27 12
numeric_clustering numeric_clustering Clustering tool for numberic values 2015-12-19 http://scikit-learn.org/stable/index.html 0.9 anaconda To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 11 1 486 0 0 0 0 0 0 0 0 3 3 4 4 490 5 14 4
openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. 2015-02-28 2.1.0 openms 3.4.1 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 583 698 30109 114383 10 10 417 417 33 34 1321 1325 0 0 0 0 116125 31847 742 626 https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=86d50bbaaa3936dc, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=da10c475c83c5469, https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5, https://usegalaxy.eu/published/workflow?id=eaf4d8f8fb3e683d, https://usegalaxy.org.au/published/workflow?id=03efeb2948494130, https://usegalaxy.org.au/published/workflow?id=236e0f306916149b, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1424?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1446?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1452?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/613?version=2 proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil
pandas_rolling_window pandas_rolling_window Rolling window calculations 2019-05-20 https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html 0.1 numpy To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12 14 115 288 25 25 68 68 0 0 0 0 0 0 0 0 356 183 39 37
parabricks_fq2bam parabricks_fq2bam Run GPU-bwa mem mapper 2025-10-15 https://github.com/bgruening/galaxytools 4.6.0-1 To update Next Gen Mappers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/parabricks_fq2bam https://github.com/bgruening/galaxytools/tree/master/tools/parabricks 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. 2016-12-02 https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ 1.5 paralyzer 1.5 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 29 256 358 0 0 0 0 0 0 0 0 0 0 0 0 358 256 29 19 https://usegalaxy.eu/published/workflow?id=a108b575b16e6cb9
partialr_square partialRsq Compute partial R square 2014-04-01 1.0.0 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 44 15 144 0 0 0 0 0 0 0 0 144 15 44 8
peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data 2018-01-30 0.2.0+galaxy1 peakachu 0.2.0 To update Sequence Analysis, RNA rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 176 217 2688 3707 0 0 0 0 0 0 0 0 0 0 0 0 3707 2688 217 176 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://workflowhub.eu/workflows/1706?version=1 transcriptomics/clipseq
pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns 2014-07-28 1.0.0 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 2 0 2 0
pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. 2023-02-02 http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ 1.6 pfam_scan 1.6 Up-to-date Sequence Analysis Protein sequence analysis Protein sequence analysis Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 146 146 7522 7522 143 143 881 881 33 33 545 545 1 1 1 1 8949 8949 323 323 https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 transcriptomics/differential-isoform-expression
pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp 2014-07-28 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pgtools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history 2017-09-28 https://www.postgresql.org postgresql To update Data Export, Data Source bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool 2022-01-28 https://pharmcat.org/ To update Variant Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 41 41 163 163 108 108 331 331 0 0 0 0 0 0 0 0 494 494 149 149
pileometh pileometh A tool for processing bisulfite sequencing alignments 2017-02-14 https://github.com/dpryan79/MethylDackel 0.5.2 methyldackel 0.6.1 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 662 1068 18187 25413 475 475 12892 12892 124 124 3414 3430 1 1 3 3 41738 34496 1668 1262 https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1566?version=1 epigenetics/methylation-seq
pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases 2015-03-06 1.0.3 bx-python 0.14.0 To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 51 68 145 687 183 1591 1254 7973 19 31 685 966 1 1 2 2 9628 2086 1691 254 https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7
pileup_parser pileup_parser Filter pileup on coverage and SNPs 2013-08-26 https://github.com/galaxyproject/tools-devteam/ 1.0.2 perl To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 473 547 3396 4352 1121 4651 7364 53190 143 332 1908 2971 4 4 196 196 60709 12864 5534 1741 https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.org.au/published/workflow?id=83c20d8e5fd97313, https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7, https://usegalaxy.org/published/workflow?id=11dac9cba49be089, https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158, https://usegalaxy.org/published/workflow?id=31dea5361ec9421c, https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1, https://usegalaxy.org/published/workflow?id=4339d5625c15ae78, https://usegalaxy.org/published/workflow?id=558c28293ec2d239, https://usegalaxy.org/published/workflow?id=578f46106f72c971, https://usegalaxy.org/published/workflow?id=6c68099053763993, https://usegalaxy.org/published/workflow?id=7c3faadda8f89749, https://usegalaxy.org/published/workflow?id=80fa8f0fe6330b88, https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986
pipmir pipmir A method to identify novel plant miRNA. 2016-11-25 https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ 0.1.0 pipmir 1.1 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 54 296 385 0 0 0 0 0 0 0 0 0 0 0 0 385 296 54 43
piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data 2015-07-02 1.2.1.0 piranha 1.2.1 To update Sequence Analysis, RNA rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 128 1127 2135 0 0 0 0 0 0 0 0 0 0 0 0 2135 1127 128 90 https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf
platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data 2015-02-28 http://www.well.ox.ac.uk/platypus 0.0.11 platypus To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plot_from_lda plot_for_lda_output1 Draw ROC plot on "Perform LDA" output 2014-07-28 1.0.1 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14 26 23 78 40 355 91 919 7 10 98 155 3 3 3 3 1155 215 394 64
plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems 2018-10-11 http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics 0.4 galaxy-ml 0.10.0 To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 212 271 1209 1809 183 197 1178 1393 26 29 770 906 0 0 0 0 4108 3157 497 421 https://usegalaxy.eu/published/workflow?id=1d55d5d20c581b16, https://usegalaxy.eu/published/workflow?id=77fa6e5a8fa3f911, https://usegalaxy.eu/published/workflow?id=fdbf1a1a584a429c, https://usegalaxy.org.au/published/workflow?id=517f947adc81a16a, https://usegalaxy.org.au/published/workflow?id=bfd7ed2abc95b53d, https://usegalaxy.org/published/workflow?id=0cf9868ebc9ec1dc, https://usegalaxy.org/published/workflow?id=728ce1ce56c4d3da, https://workflowhub.eu/workflows/1588?version=1, https://workflowhub.eu/workflows/1592?version=1 statistics/classification_machinelearning, statistics/classification_regression
plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly 2018-09-23 https://plot.ly/python/parallel-coordinates-plot/ 0.2 python To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 76 125 155 670 99 129 539 690 25 29 671 745 0 0 0 0 2105 1365 283 200 https://usegalaxy.eu/published/workflow?id=83fe480cdbb70099, https://usegalaxy.eu/published/workflow?id=c15303fcc0b53df6, https://usegalaxy.org.au/published/workflow?id=92b5a29a956a3afc, https://workflowhub.eu/workflows/1722?version=1 statistics/age-prediction-with-ml
plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems 2018-10-30 http://scikit-learn.org/stable/supervised_learning.html#supervised-learning 0.1 python To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 203 301 625 1074 134 145 555 606 30 32 239 273 0 0 0 0 1953 1419 478 367 https://usegalaxy.eu/published/workflow?id=138d4893a1d6228e, https://usegalaxy.eu/published/workflow?id=4b383d13ff512687, https://usegalaxy.eu/published/workflow?id=87546e050916dd0e, https://usegalaxy.eu/published/workflow?id=a669986e1a5cee31, https://usegalaxy.eu/published/workflow?id=a824fb7e65a1a939, https://usegalaxy.org.au/published/workflow?id=350433eefb835f19, https://usegalaxy.org.au/published/workflow?id=65a8ac91d6ded9a2, https://usegalaxy.org.au/published/workflow?id=697945d5f9edbf39, https://usegalaxy.org.au/published/workflow?id=cebab4f1a2405a89, https://usegalaxy.org/published/workflow?id=1c579fc1fe256993, https://workflowhub.eu/workflows/1583?version=1, https://workflowhub.eu/workflows/1596?version=1, https://workflowhub.eu/workflows/1633?version=1, https://workflowhub.eu/workflows/1721?version=1 statistics/FNN, statistics/age-prediction-with-ml, statistics/classification_regression, statistics/regression_machinelearning
poisson2test poisson2test Poisson two-sample test 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Statistics, Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14 18 36 122 1 140 4 562 6 8 328 437 0 0 0 0 1121 368 166 21
predictnls predictnls Python reimplementation of predictNLS for Galaxy 2013-09-23 https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
principal_component_analysis pca1 Principal Component Analysis 2014-05-19 1.0.2 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 194 270 9535 10108 519 1543 2512 8331 0 0 0 0 16 16 44 44 18483 12091 1829 729 https://usegalaxy.org/published/workflow?id=13a550ed56b56502, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=e10859cc568da07c
protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. 2016-03-13 https://github.com/fabriziocosta/eden 0.9 eden 2.0 To update Sequence Analysis, Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 26 37 168 0 0 0 0 0 0 0 0 0 0 0 0 168 37 26 18
protein_properties bg_protein_properties Calculation of various properties from given protein sequences 2015-06-07 0.2.0 biopython 1.70 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 99 123 497 720 0 0 0 0 0 0 0 0 0 0 0 0 720 497 123 99
proteomics_improviser proteomics_improviser Visualisation of PepXML files 2015-02-28 http://www.improviser.uni-freiburg.de/ 1.1.0.1 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pubchem_rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. 2015-02-28 https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html 0.1.0 To update Data Source bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime2_dbotu_q2 qiime2_dbotu_q2 q2-dbotu is a Qiime 2 plugin for performing OTU clustering 2025-03-20 https://github.com/cduvallet/q2-dbotu/tree/master 2022.11.1+galaxy0 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/ https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2 qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 7 7
quality_filter qualityFilter Filter nucleotides based on quality scores 2014-04-01 1.0.1 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 62 56 724 0 0 0 0 0 0 0 0 724 56 62 32
racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 2018-06-11 https://github.com/isovic/racon 1.5.0 racon 1.5.0 Up-to-date Sequence Analysis Genome assembly, Mapping assembly Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Whole genome sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1046 1151 32503 37525 683 683 23074 23074 263 268 9144 9214 31 31 320 320 70133 65041 2133 2023 https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a4f50449afde4a05, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=0c421197e022f323, https://usegalaxy.org.au/published/workflow?id=1ff6aabb7e3954ac, https://usegalaxy.org.au/published/workflow?id=45e9910f46a210d8, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=bcdc5ce2ea8700fc, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1599?version=1, https://workflowhub.eu/workflows/1604?version=1, https://workflowhub.eu/workflows/227?version=1, https://workflowhub.eu/workflows/228?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/563?version=1 assembly/largegenome, microbiome/plasmid-metagenomics-nanopore
rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs 2023-12-03 https://github.com/michauhl/RBPBench 0.8.1 rbpbench 1.0.6 To update Sequence Analysis, RNA, CLIP-seq RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 135 135 0 0 0 0 0 0 0 0 0 0 0 0 135 135 12 12
rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments 2017-04-13 https://github.com/BIMSBbioinfo/RCAS 1.5.4 bioconductor-rcas 1.32.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 110 718 1316 0 0 0 0 0 0 0 0 0 0 0 0 1316 718 110 89 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://workflowhub.eu/workflows/1706?version=1 transcriptomics/clipseq
rcve rcve1 Compute RCVE 2014-04-01 1.0.0 R To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 46 8 193 0 0 0 0 0 0 0 0 193 8 46 5
reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. 2015-12-09 https://github.com/chengyuan/reago-1.1 1.1 reago 1.1 Up-to-date Metagenomics, RNA Sequence assembly Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Sequence assembly, RNA, Metagenomics, Microbiology rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 7 7
remove_beginning Remove beginning1 Remove lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 4474 5036 261403 289906 4475 9406 45067 126317 1866 2086 15994 17542 295 297 1881 1952 435717 324345 16825 11110 https://usegalaxy.cz/published/workflow?id=a5241f01bb65bd38, https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=0b568c9735c03360, https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=138d4893a1d6228e, https://usegalaxy.eu/published/workflow?id=1b72af1870c540d6, 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remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation 2016-11-24 https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna 1.0.0 remurna 1.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 10 38 71 0 0 0 0 0 0 0 0 0 0 0 0 71 38 10 8
repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2015-02-28 http://www.repeatmasker.org/ 0.1.2 RepeatMasker 4.2.1 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1428 1448 10157 10293 1181 1219 9955 10202 413 413 4594 4594 91 91 610 610 25699 25316 3171 3113 https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=4a71a1e08a4a8e61, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050, https://usegalaxy.org/published/workflow?id=fb8b997f516288e1, https://workflowhub.eu/workflows/1538?version=2, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/753?version=1, https://workflowhub.eu/workflows/875?version=3 ecology/phylogeny-data-prep, genome-annotation/repeatmasker
replace_column_by_key_value_file replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. 2017-02-24 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 511 584 578207 578456 301 444 42494 44816 118 118 2392 2400 12 12 2149 2149 627821 625242 1158 942 https://usegalaxy.eu/published/workflow?id=036990ecf300a99f, https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16, https://usegalaxy.eu/published/workflow?id=0c94260298199d8b, https://usegalaxy.eu/published/workflow?id=20592f292c205954, https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312, https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb, https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=6e0330de5d80e619, https://usegalaxy.eu/published/workflow?id=70ec8b1719e25982, https://usegalaxy.eu/published/workflow?id=88f5cef7e4146520, https://usegalaxy.eu/published/workflow?id=9eb29cc96d8d75c2, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=eb03839cc36048f5, https://usegalaxy.fr/published/workflow?id=798c8ff19825ab2c, https://usegalaxy.fr/published/workflow?id=b168a179d1b456cb, https://usegalaxy.org.au/published/workflow?id=1764bb1f506212e8, https://usegalaxy.org.au/published/workflow?id=1782d699b0166725, https://usegalaxy.org.au/published/workflow?id=5a975438c8752269, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=7cc2b5010c56f117, https://usegalaxy.org.au/published/workflow?id=800d28ec61b15244, https://usegalaxy.org.au/published/workflow?id=8e2b94c6fbf44368, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org.au/published/workflow?id=989eb73372135796, https://usegalaxy.org.au/published/workflow?id=b601f48ecec15bf4, https://usegalaxy.org.au/published/workflow?id=b920b02a23f94d11, https://usegalaxy.org.au/published/workflow?id=d0d6743450e5060d, https://usegalaxy.org.au/published/workflow?id=fbc732db2a2821b0, https://usegalaxy.org/published/workflow?id=07e761b2501971c6, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2b09f3c9465ee054, https://usegalaxy.org/published/workflow?id=2dceaa255cc8cf83, https://usegalaxy.org/published/workflow?id=6c2bb2209aad5e44, https://usegalaxy.org/published/workflow?id=7af656b8ea5e7e2e, https://usegalaxy.org/published/workflow?id=8a01c78688beae1d, https://usegalaxy.org/published/workflow?id=dcbc71347300822d, https://usegalaxy.org/published/workflow?id=f58c90061c31bd48, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/109?version=9, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1566?version=1 epigenetics/methylation-seq, single-cell/scatac-standard-processing-snapatac2
ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. 2016-06-07 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ 1.3.1a ribotaper 1.3.1 To update RNA Gene expression profiling Gene expression profiling Functional genomics Functional genomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 33 38 595 798 0 0 0 0 0 0 0 0 0 0 0 0 798 595 38 33
rmap rmap_wrapper RMAP for Solexa Short Reads Alignment 2014-05-19 1.0.0 rmap 2.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores 2014-05-19 1.0.0 rmap 2.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rnabob rbc_rnabob Fast pattern searching for RNA structural motifs 2015-02-28 http://eddylab.org/software.html 2.2.1.0 rnabob 2.2.1 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10 14 55 206 0 0 0 0 0 0 0 0 0 0 0 0 206 55 14 10
rnacode rbc_rnacode Analyze the protein coding potential in MSA 2015-06-16 0.3.2 rnacode 0.3.1 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 35 31 1363 0 0 0 0 0 0 0 0 0 0 0 0 1363 31 35 12 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. 2016-05-31 https://github.com/gianlucacorrado/RNAcommender 0.1.1 sam 3.5 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 23 31 1083 0 0 0 0 0 0 0 0 0 0 0 0 1083 31 23 17
rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction 2024-07-11 https://github.com/automl/RNAformer 1.2.0 rnaformer To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 24 112 112 0 0 0 0 0 0 0 0 0 0 0 0 112 112 24 24
rnalien RNAlien RNAlien unsupervized RNA family model construction 2017-03-07 http://rna.tbi.univie.ac.at/rnalien/ 1.3.6 rnalien 1.8.0 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 14 22 34 0 0 0 0 0 0 0 0 0 0 0 0 34 22 14 8 https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
rnashapes RNAshapes Compute secondary structures of RNA 2015-02-28 3.3.0 @EXECUTABLE@ To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 60 212 284 0 0 0 0 0 0 0 0 0 0 0 0 284 212 60 43
rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs 2016-11-24 http://rth.dk/resources/rnasnp/ 1.2.0 rnasnp 1.2 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 24 46 100 0 0 0 0 0 0 0 0 0 0 0 0 100 46 24 16
rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. 2015-02-28 https://www.tbi.univie.ac.at/~wash/RNAz/ 2.1.1 rnaz 2.1.1 Up-to-date RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 37 81 251 43350 0 0 0 0 0 0 0 0 0 0 0 0 43350 251 81 37 https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1
rrna meta_rna Identification of ribosomal RNA genes in metagenomic fragments. 2015-02-28 http://weizhong-lab.ucsd.edu/meta_rna/ 0.1 hmmsearch3.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
run_jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy 2021-12-11 0.0.1 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 33 33 0 0 0 0 0 0 0 0 0 0 0 0 33 33 3 3
sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data 2015-02-28 http://www.cs.cmu.edu/~ckingsf/software/sailfish/ 0.10.1.1 bzip2 To update Sequence Analysis, RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 230 3461 4740 487 1218 7744 15838 142 205 2781 3621 2 2 57 57 24256 14043 1655 792 https://usegalaxy.org/published/workflow?id=53834a5fb46ca0f6, https://usegalaxy.org/published/workflow?id=6dada297572d77bd
salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. 2016-03-21 https://github.com/COMBINE-lab/salmon 1.10.1 salmon 1.10.3 To update Sequence Analysis, RNA, Transcriptomics, Single Cell Sequence composition calculation, RNA-Seq quantification, Gene expression analysis Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics RNA-Seq, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data 2 3 3 2 0 0 0 0 0 0 0 0 0 0 0 3 1 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 2199 2418 82278 93457 3368 5386 96508 145803 536 668 14784 19109 141 142 1347 1350 259719 194917 8614 6244 https://usegalaxy.eu/published/workflow?id=0d6bed63a2e4c3d6, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=1ffc058273ab357e, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=350d7e6976e15d30, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=65aed668233d5f73, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org.au/published/workflow?id=13a2c5bd07705985, https://usegalaxy.org.au/published/workflow?id=3f45685df9b9e792, https://usegalaxy.org.au/published/workflow?id=954318db8c8d9219, https://usegalaxy.org.au/published/workflow?id=b0614274c66efa95, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0930f955bdac93e8, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1, https://workflowhub.eu/workflows/1676?version=1, https://workflowhub.eu/workflows/1717?version=2 single-cell/scrna-case_alevin, transcriptomics/mirna-target-finder, transcriptomics/srna
sam2interval sam2interval Convert SAM to interval. 2013-08-26 1.0.2 python To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 51 67 1241 1493 137 1759 2387 19317 8 17 576 740 4 4 5 5 21555 4209 1847 200 https://usegalaxy.org/published/workflow?id=0115daec07bb1da6, https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a
sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values 2013-08-26 1.0.1 python To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 26 4 278 207 6356 1665 76071 16 32 232 403 2 2 24 24 76776 1925 6416 227 https://usegalaxy.eu/published/workflow?id=4412f7223a557b48, https://usegalaxy.org/published/workflow?id=0017c434354b6f6a, https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=165c8a58baffe64c, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=1e2e064c33b9c521, https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158, https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1, https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1, https://usegalaxy.org/published/workflow?id=3696bd8abe0f7746, https://usegalaxy.org/published/workflow?id=378159d1ad2e98f9, https://usegalaxy.org/published/workflow?id=38f5ab09779a6495, https://usegalaxy.org/published/workflow?id=4a5730954d776cb2, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=555e68f5c807ff73, https://usegalaxy.org/published/workflow?id=578f46106f72c971, https://usegalaxy.org/published/workflow?id=6172b57f4c49e364, https://usegalaxy.org/published/workflow?id=6f436066dffbc37d, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=83fbcdf3e29c41d0, https://usegalaxy.org/published/workflow?id=84aa86200ff74b4a, https://usegalaxy.org/published/workflow?id=92a233e5f2405830, https://usegalaxy.org/published/workflow?id=99e754eaabd7f362, https://usegalaxy.org/published/workflow?id=a23bf4cd3bc97f2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=b4bb2c7d8c7b5139, https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a, https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907, https://usegalaxy.org/published/workflow?id=ca5ca2f38c1719e1, https://usegalaxy.org/published/workflow?id=e35ac40c58953f74, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986, https://usegalaxy.org/published/workflow?id=ea817818a6de77e0, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f3983646b6df24bf
sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! 2016-06-23 https://github.com/biod/sambamba 1.0.1 sambamba 1.0.1 Up-to-date SAM bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 229 229 6620 6620 0 0 0 0 0 0 0 0 0 0 0 0 6620 6620 229 229 https://usegalaxy.eu/published/workflow?id=d92f9c33dded693f, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2
sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 376 457 3760 4585 274 274 2029 2029 54 54 2601 2601 9 9 113 113 9328 8503 794 713 transcriptomics/mirna-target-finder
samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) 2014-04-14 http://www.htslib.org/ 0.0.5 samtools 1.22.1 To update Assembly, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
samtools_depth samtools_depth Coverage depth via samtools 2014-11-19 http://www.htslib.org/ 0.0.3 samtools 1.22.1 To update Assembly, Sequence Analysis, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1071 1130 8403 9175 1771 1964 11692 12814 99 99 761 761 77 77 151 151 22901 21007 3270 3018 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=38f57cffaeb0e39f, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=06d6dcd2655592af, https://usegalaxy.org/published/workflow?id=18899840e49d89c3, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=3f2d1003ff959c7c, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://usegalaxy.org/published/workflow?id=8daa91d54040ba95, https://usegalaxy.org/published/workflow?id=b561d3d9645a2726, https://usegalaxy.org/published/workflow?id=c4af6c5f5dfaae82, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://usegalaxy.org/published/workflow?id=f3ed710e251833a7, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1, https://workflowhub.eu/workflows/1738?version=1, https://workflowhub.eu/workflows/1739?version=1, https://workflowhub.eu/workflows/1740?version=1, https://workflowhub.eu/workflows/1741?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data
samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) 2013-11-11 http://www.htslib.org/ 0.0.6 samtools 1.22.1 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5115 5963 62930 71062 8050 12101 84370 129360 1344 1722 18420 20536 473 475 2848 2865 223823 168568 20261 14982 https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=25aa944237d7fb82, https://usegalaxy.eu/published/workflow?id=2f51a82838722bec, https://usegalaxy.eu/published/workflow?id=30e7dc81e323cbdb, https://usegalaxy.eu/published/workflow?id=36a4646959829018, 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sed_wrapper sed_stream_editor Manipulate your data with the sed command line tool. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 53 43 2284 0 0 0 0 0 0 0 0 0 0 0 0 2284 43 53 6 https://usegalaxy.eu/published/workflow?id=04dbf1e548db74fd, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4
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seq_composition seq_composition Sequence composition 2014-08-12 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 176 237 1521 1668 253 253 816 816 0 0 0 0 4 4 47 47 2531 2384 494 433 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6
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seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files 2014-11-04 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 190 242 4624 5314 0 0 0 0 0 0 0 0 0 0 0 0 5314 4624 242 190 https://usegalaxy.eu/published/workflow?id=9668976304efea5c
seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) 2018-05-08 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 To update Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_primer_clip seq_primer_clip Trim off 5' or 3' primers 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 To update Assembly, Fasta Manipulation, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_rename seq_rename Rename sequences with ID mapping from a tabular file 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_select_by_id seq_select_by_id Select sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 259 303 1772 3868 10 12 435 499 4367 2207 315 269
short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads 2014-05-19 1.0.0 rpy To update Sequence Analysis, Graphics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
short_reads_figure_score quality_score_distribution Build base quality distribution 2014-05-19 1.0.2 fontconfig To update Sequence Analysis, Graphics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 30 71 163 5 711 67 3360 0 0 0 0 0 0 0 0 3523 138 741 28
short_reads_trim_seq trim_reads Select high quality segments 2014-05-19 1.0.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39 60 85 220 59 1608 210 6669 0 0 0 0 0 0 0 0 6889 295 1668 98 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
show_beginning Show beginning1 Select lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 0 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 2470 3456 175984 186535 4485 20035 20107 91558 499 632 3332 4032 155 156 562 666 282791 199985 24279 7609 https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=04b838103aed1929, https://usegalaxy.eu/published/workflow?id=1ac5745645634825, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=272e9106e50c9fe6, https://usegalaxy.eu/published/workflow?id=29346872085adf1f, https://usegalaxy.eu/published/workflow?id=2f7149d02db43b7b, https://usegalaxy.eu/published/workflow?id=3e91f8417a66d02c, 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https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3, https://usegalaxy.org/published/workflow?id=ffd718437128bce2, https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1392?version=1, https://workflowhub.eu/workflows/1486?version=1, https://workflowhub.eu/workflows/1561?version=1, https://workflowhub.eu/workflows/1601?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1745?version=2 data-science/data-manipulation-olympics, galaxy-interface/workflow-editor, introduction/data-manipulation-olympics, single-cell/scatac-batch-correction-snapatac2, statistics/flexynesis_classification, transcriptomics/rna-seq-analysis-clustering-viz, variant-analysis/aiv-analysis
show_tail Show tail1 Select lines from the end of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 0 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 403 680 1739 3020 687 2020 10501 25260 86 112 1390 1544 17 18 67 87 29911 13697 2830 1193 https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=3a92253f57e553bd, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=f806893fbe065406, https://workflowhub.eu/workflows/625?version=27
sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions 2014-01-27 https://home.gwu.edu/~wpeng/Software.htm 1.1 SICER 1.1 Up-to-date ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 25 45 136 394 120 1019 626 9100 5 7 640 865 3 3 5 5 10364 1407 1074 153
sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn 2016-05-02 http://scikit-learn.org 1.0.11.0 To update Machine Learning, Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 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snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data 2014-07-28 1.0.1 R To update Variant Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 14 21 50 68 199 278 700 11 23 218 303 0 0 0 0 1053 517 236 90
sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 2015-02-28 http://bioinfo.lifl.fr/RNA/sortmerna/ 4.3.6 sortmerna 4.3.7 To update RNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics Metatranscriptomics, Metagenomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1135 1352 23920 26406 581 581 6479 6479 219 225 3668 3882 116 116 648 651 37418 34715 2274 2051 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://workflowhub.eu/workflows/1444?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
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sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data 2018-07-05 https://github.molgen.mpg.de/heller/ssHMM 1.0.7 sshmm 1.0.7 Up-to-date Sequence Analysis, RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 20 156 228 0 0 0 0 0 0 0 0 0 0 0 0 228 156 20 15
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substitution_rates subRate1 Estimate substitution rates for non-coding regions 2014-04-01 1.0.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 747 12 3901 3 4 61 114 0 0 0 0 4015 73 751 7
substitutions substitutions1 Fetch substitutions from pairwise alignments 2014-04-01 1.0.1 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 84 41 901 0 0 0 0 0 0 0 0 901 41 84 10
subtract gops_subtract_1 Subtract the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 418 512 568334 569352 1292 7771 48668 186026 130 191 20401 21159 8 9 1165 1175 777712 638568 8483 1848 https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.eu/published/workflow?id=d52ff93f4ffdd981, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=61a21c9928182ae4, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=5834e562fa403732, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=66748e20a243eafe, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=7bc71a005c6f18d0, https://usegalaxy.org/published/workflow?id=b1cd3f793187d667, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/356?version=1
subtract_query subtract_query1 Subtract Whole Dataset from another dataset 2014-04-01 https://github.com/galaxyproject/gops 0.1 bx-python 0.14.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 126 162 1385 1863 544 3501 2449 40799 20 39 786 1156 18 20 148 172 43990 4768 3722 708 https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.org/published/workflow?id=0115daec07bb1da6, https://usegalaxy.org/published/workflow?id=a3de4b3f7b910059, https://usegalaxy.org/published/workflow?id=b2176abeb937f026
sylph sylph_profile, sylph_query sylph - fast and precise species-level metagenomic profiling with ANIs 2024-10-08 https://github.com/bluenote-1577/sylph 0.8.1 sylph 0.9.0 To update Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/main/tools/sylph https://github.com/bgruening/galaxytools/tree/master/tools/sylph sylph sylph fast and precise species-level metagenomic profiling with ANIs 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 257 257 1 1 1 1 0 0 0 0 1 1 12 12 270 270 11 11 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7
t2ps Draw_phylogram Draw phylogeny 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Metagenomics Phylogenetic tree visualisation Phylogenetic tree visualisation Phylogenomics Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps t2ps Draw phylogeny "Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 64 93 405 479 13 1240 102 7952 0 0 0 0 0 0 0 0 8431 507 1333 77 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
t2t_report t2t_report Summarize taxonomy 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.1 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 82 745 1071 16 1143 118 7194 0 0 0 0 0 0 0 0 8265 863 1225 71 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c
t_test_two_samples t_test_two_samples T Test for Two Samples 2013-09-25 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 37 54 238 74 290 279 1220 10 12 1020 1390 3 3 4 4 2852 1357 342 110
table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered 2013-12-02 0.2 annovar To update Variant Analysis devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1589 7466 9066 64545 0 0 0 0 0 0 0 0 64545 9066 7466 1589 https://usegalaxy.org/published/workflow?id=02755c14619242da, https://usegalaxy.org/published/workflow?id=049e6609da2b67c4, https://usegalaxy.org/published/workflow?id=0660a00407fc16a1, https://usegalaxy.org/published/workflow?id=0843c6f15eae2f15, https://usegalaxy.org/published/workflow?id=0a89328e6d28dd07, https://usegalaxy.org/published/workflow?id=0d8eb75d28fa7df2, https://usegalaxy.org/published/workflow?id=10d8d47f97afc999, https://usegalaxy.org/published/workflow?id=17a7ff756d37a437, 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tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 perl To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 31 42 2041 2227 0 0 0 0 0 0 0 0 4 5 79 89 2316 2120 47 35 https://workflowhub.eu/workflows/789?version=1
tabpfn tabpfn Tabular data prediction using TabPFN using Pytorch. 2024-10-14 https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn 2.0.9 tabpfn To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 218 218 0 0 0 0 0 0 0 0 0 0 0 0 218 218 8 8 https://workflowhub.eu/workflows/1873?version=1 statistics/flexynesis_classification
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targetfinder targetfinder Plant small RNA target prediction tool 2015-10-23 https://github.com/carringtonlab/TargetFinder.git 1.7 targetfinder 1.7 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 137 935 990 99 99 340 340 34 34 1290 1290 0 0 0 0 2620 2565 270 262 https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://workflowhub.eu/workflows/1717?version=2 transcriptomics/mirna-target-finder
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tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. 2021-11-14 https://github.com/BGI-Qingdao/TGS-GapCloser 1.0.3 tgsgapcloser 1.2.1 To update Assembly Genome assembly, Read mapping, Scaffolding, Localised reassembly Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 67 67 587 587 0 0 0 0 0 0 0 0 0 0 0 0 587 587 67 67
tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. 2024-05-23 https://github.com/ibe-uw/tiara 1.0.3 tiara To update Metagenomics, Sequence Analysis Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation Sequencing, Genomics, DNA polymorphism bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 33 365 365 0 0 0 0 0 0 0 0 0 0 0 0 365 365 33 33
tmhmm_and_signalp promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb 2010-10-21 https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 520 587 12727 14764 1 1 2 2 0 0 0 0 0 1 0 6 14772 12729 589 521 https://usegalaxy.eu/published/workflow?id=3280dc48d768b46a, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://workflowhub.eu/workflows/1417?version=1 proteomics/secretome-prediction
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tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step 2014-01-27 0.1 blast+ To update Transcriptomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 36 49 191 251 1 191 2 814 4 12 85 120 0 0 0 0 1185 278 252 41
trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer 2015-02-28 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 0.6.10 trim-galore 0.6.10 Up-to-date Sequence Analysis, Fastq Manipulation Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6966 8378 297289 379413 13276 20041 284172 418931 1722 2020 36616 41727 303 305 3334 3366 843437 621411 30744 22267 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trimmer trimmer Trim leading or trailing characters. 2012-12-04 0.0.1 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 561 669 7246 10121 602 3059 10190 111036 69 104 578 1181 11 12 37 57 122395 18051 3844 1243 https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=250e6058f160825f, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=7c80cd57b2de54d4, https://usegalaxy.eu/published/workflow?id=933ab5e7fe13a8e0, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.org/published/workflow?id=08edef22fa132799, https://usegalaxy.org/published/workflow?id=0a3513961f0cf9dd, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=3edea70fbdb9dbd9, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=e107d8036c064616, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22
trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. 2015-02-28 http://mbioserv2.mbioekol.lu.se/ARAGORN/ 0.6 aragorn 1.2.41 To update RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 513 608 7300 7928 0 0 0 0 111 120 2476 2875 0 0 0 0 10803 9776 728 624 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178
ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser 2014-07-28 1.0.1 python To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 148 182 436 579 586 4184 2240 19093 0 0 0 0 0 1 0 10 19682 2676 4367 734 https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=7878623b7e959284, https://usegalaxy.org/published/workflow?id=4782a4943b6fa990
uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval 2015-10-09 https://github.com/jdrudolph/uniprot 0.7 requests To update Proteomics, Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 387 494 2533 3404 532 1083 2598 6109 97 97 1129 1129 0 0 0 0 10642 6260 1674 1016 https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://workflowhub.eu/workflows/1417?version=1, https://workflowhub.eu/workflows/1426?version=1 proteomics/maxquant-msstats-dda-lfq, proteomics/secretome-prediction
unique bg_uniq This tool returns all unique lines from a tab-separated file. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 537 648 6125 9172 0 0 0 0 0 0 0 0 83 83 492 492 9664 6617 731 620 https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=516b4d4146e4af66, https://usegalaxy.eu/published/workflow?id=6064d1dd87b458be, https://usegalaxy.eu/published/workflow?id=6f4bbed7a320dc2f, https://usegalaxy.eu/published/workflow?id=836cc09d17eaecb0, https://usegalaxy.eu/published/workflow?id=b46b51b2860b63d5, https://usegalaxy.eu/published/workflow?id=c9423228df977254, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4, https://workflowhub.eu/workflows/117?version=1, https://workflowhub.eu/workflows/1417?version=1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 assembly/metagenomics-assembly, ecology/ENA_Biodiv_submission, genome-annotation/bacterial-comparative-genomics-dataset-construction, microbiome/metagenomics-assembly, proteomics/secretome-prediction
varscan_version_2 varscan VarScan wrapper 2013-11-17 https://dkoboldt.github.io/varscan/ 2.4.2 varscan 2.4.6 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 626 819 7561 9274 2644 6123 14138 55924 441 534 2664 3327 45 45 153 153 68678 24516 7521 3756 https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2, https://usegalaxy.org/published/workflow?id=683a0ab042fa34c9, https://usegalaxy.org/published/workflow?id=80b12b6e7ac8861f, https://usegalaxy.org/published/workflow?id=9a1b4c9747bf6ae0, https://usegalaxy.org/published/workflow?id=a37961bf3d435918, https://usegalaxy.org/published/workflow?id=a765dc267c6a5c3a, https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9, https://usegalaxy.org/published/workflow?id=a7ee7de93a7fb261, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86
vcf2pgsnp vcf2pgSnp VCF to pgSnp 2014-07-28 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 72 163 241 172 614 1040 2765 0 0 0 0 0 0 0 0 3006 1203 686 229
vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 23 54 160 340 0 0 0 0 342 160 56 23
vcf_extract vcf_extract Extract reads from a specified region 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 9 308 569 0 0 0 0 569 308 9 5
vcf_filter vcf_filter Filter a VCF file 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 183 199 494 630 0 0 0 0 15 56 147 606 0 0 0 0 1236 641 255 198
vcf_intersect vcf_intersect Generate the intersection of two VCF files 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 19 0 0 0 0 16 28 204 463 0 0 0 0 482 204 31 16
vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations 2013-11-24 https://vcftools.github.io/ 0.1 echo To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 95 127 179 280 640 1445 2025 4484 7 16 75 156 3 3 3 3 4923 2282 1591 745 https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9, https://usegalaxy.org/published/workflow?id=e7586d70715207b5, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86
vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics 2013-11-24 https://vcftools.github.io/ 0.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 181 461 726 0 0 0 0 0 12 0 16 0 0 0 0 742 461 193 138
vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence 2016-10-16 https://vcftools.github.io/ 0.1.11 samtools 1.22.1 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vcftools_isec vcftools_isec Intersect multiple VCF datasets 2013-11-24 https://vcftools.github.io/ 0.1.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 110 144 370 622 0 1 0 1 28 50 43 504 0 0 0 0 1127 413 195 138 https://usegalaxy.org.au/published/workflow?id=3d5deed70ac9bde4
vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset 2013-11-24 https://vcftools.github.io/ 0.1.11 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 285 342 1115 1467 1 1 1 1 50 72 112 481 0 0 0 0 1949 1228 415 336 https://usegalaxy.eu/published/workflow?id=c00fe92f9a579a15
vcftools_slice vcftools_slice Subset VCF dataset by genomic regions 2013-11-24 https://vcftools.github.io/ 0.1 echo To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 58 73 445 502 127 381 538 8328 7 19 75 157 0 1 0 5 8992 1058 474 192
vcftools_subset vcftools_subset Select samples from a VCF dataset 2013-11-24 https://vcftools.github.io/ 0.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 51 94 147 0 0 0 0 8 19 71 142 0 0 0 0 289 165 70 48
venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 764 928 7475 8987 955 2175 9138 19328 0 0 0 0 27 27 117 117 28432 16730 3130 1746 https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960
viennarna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures 2015-02-28 http://www.tbi.univie.ac.at/RNA/ 2.2.10 viennarna 2.7.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 155 209 2275 8658 0 0 0 0 0 0 0 0 0 0 0 0 8658 2275 209 155 https://usegalaxy.eu/published/workflow?id=58fd339165ded462, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7
vpt vpt_extract, vpt_segment Vizgen Post-processing Tool 2025-04-29 https://vizgen.github.io/vizgen-postprocessing/ 1.3.0 To update Single Cell, Spatial Omics, Transcriptomics, Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/vpt https://github.com/bgruening/galaxytools/tree/master/tools/vpt 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 29 29 0 0 0 0 0 0 0 0 0 0 0 0 29 29 3 3
vrhyme vrhyme Tool for dereplication and binning virus genomes from metagenomes. 2025-05-14 https://github.com/AnantharamanLab/vRhyme 1.1.0 vrhyme 1.1.0 Up-to-date Metagenomics Scaffolding, Read binning, Read mapping, Sequence trimming Scaffolding, Read binning, Read mapping, Sequence trimming Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme vRhyme vRhyme vRhyme enables binning of viral genomes from metagenomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 6 6
vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. 2015-02-28 0.2 vt 2015.11.10 To update Sequence Analysis, Variant Analysis bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval 2014-04-01 1.0.1 galaxy-ops 1.1.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 76 119 2308 0 0 0 0 0 0 0 0 2308 119 76 10
whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. 2024-04-23 https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 388 388 0 0 0 0 0 0 0 0 0 0 0 0 388 388 27 27 https://usegalaxy.eu/published/workflow?id=a2284469005518e1
whisperx whisperx Transcribe audio or video files to text using the OpenAI Whisper and speaker diarization using pyannote audio 2025-07-01 https://github.com/bgruening/galaxytools/tree/master/tools/whisperx 3.4.2 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisperx https://github.com/bgruening/galaxytools/tree/master/tools/whisperx 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 87 87 0 0 0 0 0 0 0 0 0 0 0 0 87 87 9 9
windowsplitter winSplitter Make windows 2014-04-01 1.0.1 bx-python 0.14.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 11 37 335 143 3983 0 0 0 0 0 0 0 0 3994 143 337 37
wordcloud wordcloud A little word cloud generator in Python. 2024-12-13 https://github.com/amueller/word_cloud 1.9.4 wordcloud To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 29 190 190 0 0 0 0 2 2 46 46 0 0 0 0 236 236 31 31 https://usegalaxy.eu/published/workflow?id=0b568c9735c03360, https://usegalaxy.eu/published/workflow?id=3a25999d71a2343a, https://usegalaxy.eu/published/workflow?id=c917db7d7ba7ea6f, https://workflowhub.eu/workflows/1623?version=1, https://workflowhub.eu/workflows/1884?version=1, https://workflowhub.eu/workflows/1953?version=1, https://workflowhub.eu/workflows/1964?version=1 digital-humanities/introduction_to_dh, digital-humanities/open-refine-tutorial, digital-humanities/text_mining_chinese
wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. 2018-06-12 https://github.com/ruanjue/wtdbg2 2.5 wtdbg 2.5 Up-to-date Assembly Genome assembly, De-novo assembly Genome assembly, De-novo assembly Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 366 451 1313 1904 0 0 0 0 0 0 0 0 28 28 145 145 2049 1458 479 394
xy_plot XY_Plot_1 Plotting tool for multiple series and graph types 2013-09-25 1.0.2 r-base To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1 1 1 1 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 818 1006 4398 6497 1927 3998 5925 16639 597 680 2952 3388 101 101 344 344 26868 13619 5785 3443 https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=25850714d13f0b0f, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=5877e2d5eba79f36, https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://usegalaxy.org/published/workflow?id=67080f040e855990, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=746f4eef47648b26, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=c50f10ecd1ac2ff9, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda, https://workflowhub.eu/workflows/1412?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/652?version=1 microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short
yolo json2yolosegment, yolo_predict, yolo_training tools for building yolo workflows. 2025-06-12 https://github.com/bgruening/galaxytools 8.3.0 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 166 166 0 0 0 0 0 0 0 0 0 0 0 0 166 166 6 6 https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://workflowhub.eu/workflows/1840?version=1 imaging/yolo-segmentation-training
AMRFinderPlus amrfinderplus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. 2023-05-12 https://github.com/ncbi/amr 3.12.8 ncbi-amrfinderplus 4.0.23 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus amrfinderplus AMRFinderPlus AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 953 953 45130 45130 689 689 17362 17362 0 0 0 0 28 28 1863 1863 64355 64355 1670 1670 https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8
Beacon2_Import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. 2024-07-22 https://pypi.org/project/beacon2-import/ 2.2.4 beacon2-import 2.2.4 Up-to-date Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 61 61 0 0 0 0 1 1 170 170 0 0 0 0 231 231 8 8 variant-analysis/beacon_cnv_query, variant-analysis/beaconise_1000hg
ISEScan isescan "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." 2022-09-01 https://github.com/xiezhq/ISEScan 1.7.3 isescan 1.7.3 Up-to-date Sequence Analysis Structural variation detection Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation Genomics, Sequence analysis, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 392 392 67516 67516 237 237 1535 1535 116 116 7464 7464 37 37 1759 1759 78274 78274 782 782 https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/bacterial-genome-annotation
abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes 2016-07-29 https://github.com/tseemann/abricate 1.0.1 abricate 1.0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Genomics, Microbiology Genomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 4522 4679 799841 821957 3401 3468 401550 405363 1867 2216 578174 600408 85 85 19178 19178 1846906 1798743 10448 9875 https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/470?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data
abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes 2023-04-03 https://zenodo.org/record/7370628 1.0.19 abritamr 1.0.19 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 319 319 2633 2633 0 0 0 0 97 97 880 880 3 3 5 5 3518 3518 419 419 https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://workflowhub.eu/workflows/634?version=1
abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 http://www.bcgsc.ca/platform/bioinfo/software/abyss 2.3.10 abyss 2.3.10 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1258 1368 7148 7779 183 414 505 1305 398 398 2608 2608 11 11 16 16 11708 10277 2191 1850
adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. 2022-05-04 https://github.com/MikkelSchubert/adapterremoval 2.3.4 adapterremoval 2.3.4 Up-to-date Fasta Manipulation, Sequence Analysis Sequence trimming, Sequence merging, Primer removal Sequence trimming, Sequence merging, Primer removal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 108 108 841 841 0 0 0 0 0 0 0 0 0 0 0 0 841 841 108 108
add_input_name_as_column addName Add input name as column on an existing tabular file 2020-03-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.2.0 python To update Text Manipulation mvdbeek https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 260 306 87241 99370 296 466 27850 30946 34 34 2760 2760 0 0 0 0 133076 117851 806 590 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=098f43ded1b5fa7f, https://usegalaxy.eu/published/workflow?id=16418e8b023ff226, https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=31c6dcd3a25620df, https://usegalaxy.eu/published/workflow?id=389d992ff7268247, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=8d00a8b70b0c019c, https://usegalaxy.eu/published/workflow?id=9aa290ce1927d700, https://usegalaxy.eu/published/workflow?id=9c5a0596956064a6, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=cc385bd4376a907c, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.eu/published/workflow?id=df99c8a88309918e, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.org.au/published/workflow?id=2df1d32f78974528, https://usegalaxy.org.au/published/workflow?id=2fee25e188531691, https://usegalaxy.org.au/published/workflow?id=446ba22c3d2f3367, https://usegalaxy.org.au/published/workflow?id=499245b3a113e06d, https://usegalaxy.org.au/published/workflow?id=518d27f68e05a356, https://usegalaxy.org.au/published/workflow?id=66e530368fd40abd, https://usegalaxy.org.au/published/workflow?id=9016b2be61f89053, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=cf775b8ff0745456, https://usegalaxy.org.au/published/workflow?id=e2c49586dc941f38, https://usegalaxy.org.au/published/workflow?id=e6552643a3713b50, https://usegalaxy.org/published/workflow?id=1e264fc06d87899f, https://usegalaxy.org/published/workflow?id=44bcae0e352563f9, https://usegalaxy.org/published/workflow?id=450c2181f89e6b23, https://usegalaxy.org/published/workflow?id=48dd4a4cb5536670, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://usegalaxy.org/published/workflow?id=768cee70d9aa8cc6, https://usegalaxy.org/published/workflow?id=b1b4fc510099d592, https://usegalaxy.org/published/workflow?id=bf79271a438ffa54, https://usegalaxy.org/published/workflow?id=e50e36a25bae863c, https://usegalaxy.org/published/workflow?id=f18e6fa5270fcd37, https://workflowhub.eu/workflows/1057?version=9, https://workflowhub.eu/workflows/1564?version=1 evolution/mtb_transmission
aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers 2021-01-03 https://github.com/BrendelGroup/AEGeAn 0.16.0 aegean 0.16.0 Up-to-date Transcriptomics, Sequence Analysis Sequence annotation Sequence annotation Sequence analysis, Gene structure Sequence analysis, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean gaeval GAEVAL Gene Annotation EVAluation. 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 69 69 291 291 57 57 117 117 33 33 2747 2747 22 22 52 52 3207 3207 181 181 https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/754?version=1 genome-annotation/funannotate
aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account 2022-06-29 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.38.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 356 356 0 0 0 0 0 0 0 0 0 0 0 0 356 356 64 64
allegro allegro Linkage and haplotype analysis from deCODE 2017-11-19 http://www.decode.com/software/ 2 allegro 3 To update Variant Analysis Sequence motif discovery Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA Sequence analysis, Transcription factors and regulatory sites, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
amplican amplican AmpliCan is an analysis tool for genome editing. 2021-09-22 https://github.com/valenlab/amplican 1.14.0 bioconductor-amplican 1.28.0 To update Sequence Analysis Alignment, Standardisation and normalisation Alignment, Standardisation and normalisation PCR experiment, Statistics and probability PCR experiment, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 85 85 0 0 0 0 0 0 0 0 0 0 0 0 85 85 18 18
ampligone ampligone AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. 2025-07-29 https://rivm-bioinformatics.github.io/AmpliGone/latest/ 2.0.1 AmpliGone 2.0.1 Up-to-date Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_export_otu, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 2022-04-04 https://github.com/MadsAlbertsen/ampvis2/ 2.8.9 To update Metagenomics Analysis, Visualisation Analysis, Visualisation Biodiversity Biodiversity iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. 1 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 56 56 3292 3292 15 15 28 28 0 0 0 0 0 0 0 0 3320 3320 71 71 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b4ed2a3690da0196, https://usegalaxy.eu/published/workflow?id=e91def3fc9738ebb, https://usegalaxy.org/published/workflow?id=82973143b28bb767, https://usegalaxy.org/published/workflow?id=b76c55dafd44b305, https://workflowhub.eu/workflows/1275?version=2, https://workflowhub.eu/workflows/1855?version=1 microbiome/mgnify-amplicon
ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. 2022-07-16 https://github.com/FrederickHuangLin/ANCOMBC 1.4.0 bioconductor-ancombc 2.8.0 To update Metagenomics DNA barcoding DNA barcoding Microbial ecology, Metagenomics, Taxonomy Microbial ecology, Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 64 64 0 0 0 0 0 0 0 0 0 0 0 0 64 64 20 20
anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects 2019-03-21 https://anndata.readthedocs.io 0.10.9 anndata 0.6.22.post1 To update Single Cell, Spatial Omics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata anndata anndata From https://anndata.readthedocs.io/en/latest/"Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray." 5 5 5 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 787 890 47423 51315 459 467 23370 23451 139 141 11736 12386 2 2 56 56 87208 82585 1500 1387 https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=21315ffd2df2f159, 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https://workflowhub.eu/workflows/646?version=2 single-cell/bulk-music-2-preparescref, single-cell/pseudobulk-analysis, single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-case_trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-plant, single-cell/scrna-scanpy-pbmc3k
anndata2ri anndata2ri Convert between Anndata and SingCellExperiment objects 2025-02-12 https://github.com/theislab/anndata2ri 1.3.2 anndata2ri 2.0 To update Single Cell, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata2ri https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata2ri anndata2ri anndata2ri RPy2 converter from AnnData to SingleCellExperiment and back. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 8 8
annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages 2017-11-17 https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.20.0 To update Genome annotation Annotation Annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3392 3780 31980 37238 6704 7867 62133 78958 1250 1315 6352 7039 25 25 181 181 123416 100646 12987 11371 https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0f7acf235096b708, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=36eefcc25ab1fe15, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=a6290cdfa12d34ad, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=d9f8c5d575da02b1, https://usegalaxy.eu/published/workflow?id=f98f0e0c18222cc0, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=93bfbd7db42db543, https://workflowhub.eu/workflows/1542?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/689?version=1 single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes
argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database 2024-08-28 https://github.com/BigDataBiology/argNorm 1.0.0 argnorm 1.1.0 To update Genome annotation Gene functional annotation Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 48 48 211 211 0 0 0 0 0 0 0 0 3 3 91 91 302 302 51 51
arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR 2022-07-27 https://github.com/suhrig/arriba 2.5.1 arriba 2.5.1 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 75 75 4142 4142 20 20 254 254 16 16 503 503 0 0 0 0 4899 4899 111 111 https://usegalaxy.eu/published/workflow?id=d0a809f0880d7ec0, https://usegalaxy.org.au/published/workflow?id=0dff588f31f1dfd6, https://usegalaxy.org.au/published/workflow?id=65250d6b30d4bc7c, https://usegalaxy.org.au/published/workflow?id=d5a3fd1faa3f0a41, https://usegalaxy.org/published/workflow?id=39810594e5c332d5, https://usegalaxy.org/published/workflow?id=b28789b6a0e1f5c9, https://workflowhub.eu/workflows/1442?version=1, https://workflowhub.eu/workflows/1792?version=1 proteomics/neoantigen-fusion-database-generation
art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data 2015-02-11 http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ 2014.11.03.0 art 2016.06.05 To update Sequence Analysis, Data Source Conversion Conversion Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 36 398 398 1 1 2 2 0 0 0 0 0 0 0 0 400 400 37 37
artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building 2020-04-17 https://github.com/artic-network/fieldbioinformatics 1.7.3 artic 1.8.5 To update Sequence Analysis Sequence alignment Sequence alignment Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 206 206 13444 13459 0 0 0 0 34 34 1812 1812 0 0 0 0 15271 15256 240 240 https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://workflowhub.eu/workflows/521?version=1
assembly_stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. 2023-06-21 https://github.com/rjchallis/assembly-stats 17.02 rjchallis-assembly-stats 17.02 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 32 32 32 32 18 18
astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees 2024-08-28 https://github.com/smirarab/ASTRAL 5.7.8 astral-tree 5.7.8 Up-to-date Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 5 5 151 151 0 0 0 0 151 151 5 5 https://workflowhub.eu/workflows/359?version=1
augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 2017-10-05 http://bioinf.uni-greifswald.de/augustus/ 3.5.0 augustus 3.5.0 Up-to-date Sequence Analysis Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families Gene transcripts, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1917 2188 16670 19094 2787 2897 18204 19188 496 496 8640 8666 49 49 4693 4693 51641 48207 5630 5249 https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://workflowhub.eu/workflows/1504?version=1 genome-annotation/annotation-with-maker
autobigs autobigs-cli Automated MLST typing from PubMLST and InstitutPasteur. 2025-02-24 https://github.com/Syph-and-VPD-Lab/autoBIGS.cli 0.6.2 autobigs-cli 0.6.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs AutoBIGS.CLI AutoBIGS.CLI A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 53 53 0 0 0 0 0 0 0 0 0 0 0 0 53 53 31 31
b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. 2022-08-09 https://bio2byte.be 3.0.5+galaxy0 b2btools 3.0.7 To update Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology Protein disorder prediction, Protein secondary structure prediction, Protein feature detection Protein disorder prediction, Protein secondary structure prediction iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 22 22 380 380 0 0 0 0 0 0 0 0 0 0 0 0 380 380 22 22
bakta bakta "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." 2022-09-01 https://github.com/oschwengers/bakta 1.9.4 bakta 1.11.4 To update Sequence Analysis Genome annotation Genome annotation Genomics, Sequence analysis, Bioinformatics Genomics, Sequence analysis, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1503 1503 67465 67465 1017 1017 14351 14351 399 399 33530 33530 84 84 3664 3664 119010 119010 3003 3003 https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation
bam2fastx bam2fastx Convert PacBio Bam File to fasta or fastq file 2024-03-11 https://github.com/PacificBiosciences/pbtk 3.5.0 pbtk 3.5.0 Up-to-date Convert Formats, Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 180 180 69 69 372 372 14 14 80 80 0 0 0 0 632 632 136 136
bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. 2015-12-07 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx 1.0.1 openjdk To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10 21 26 132 37 213 186 791 0 0 0 0 0 0 0 0 923 212 234 47
bamtools bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.3 To update Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 4 4 4 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 385 385 42883 42883 247 247 6842 6842 24 24 379 379 3 3 16 16 50120 50120 659 659 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1492?version=2 microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/aiv-analysis
bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.3 To update Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 583 746 13272 15936 1177 5735 56981 102230 6 6 283 283 14 14 56 56 118505 70592 6501 1780 https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.3 To update Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3441 4000 113566 150142 6066 11844 91327 161400 565 622 8452 9127 521 523 2536 2611 323280 215881 16989 10593 https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, 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single-cell/scrna-preprocessing, variant-analysis/non-dip, variant-analysis/somatic-variants
bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. 2021-03-29 https://github.com/statgen/bamUtil bamutil 1.0.15 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 23 23 51 51 23 23 71 71 1 1 408 408 0 0 0 0 530 530 47 47
bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily 2018-09-06 https://github.com/rrwick/Bandage 2022.09 bandage_ng 2025.6.1 To update Visualization Sequence assembly visualisation Sequence assembly visualisation Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 5065 5359 74766 78507 4846 5038 63998 65491 3140 3234 25266 26126 317 319 9763 9780 179904 173793 13950 13368 https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=01fe4c590e608103, https://usegalaxy.eu/published/workflow?id=03be9d62e8e4a129, https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=085c3a4c89d137b5, https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511, https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=1151052f4393852a, https://usegalaxy.eu/published/workflow?id=1483534f49b826bf, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=17b0a6d3379a4392, https://usegalaxy.eu/published/workflow?id=194a05d42687b524, 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barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes 2019-02-21 https://bitbucket.org/princeton_genomics/barcode_splitter/ 0.18.4.0 barcode_splitter 0.18.6 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 2023-09-06 https://github.com/lldelisle/baredSC 1.1.3 baredsc 1.1.3 Up-to-date Single Cell, Transcriptomics, Visualization Data retrieval, Expression correlation analysis, Differential gene expression profiling Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 6 6 115 115 12 12 180 180 1 1 336 336 0 0 0 0 631 631 19 19 https://usegalaxy.eu/published/workflow?id=2da3c41ad5c11c3b, https://usegalaxy.eu/published/workflow?id=3410a75a2a4899dc, https://usegalaxy.eu/published/workflow?id=4025b5dca188e6a4, https://usegalaxy.eu/published/workflow?id=49d913cefc5daaf3, https://usegalaxy.eu/published/workflow?id=4eb8aec8a5be98b3, https://usegalaxy.eu/published/workflow?id=72c03f7b5bc9fb9d, https://usegalaxy.eu/published/workflow?id=7341ca7572447d60, https://usegalaxy.eu/published/workflow?id=967f890c0883f72a, https://usegalaxy.eu/published/workflow?id=b3d38025c7ff72ed, https://usegalaxy.eu/published/workflow?id=cdf782de6c67477a, https://usegalaxy.eu/published/workflow?id=da41880826c3d758, https://usegalaxy.eu/published/workflow?id=fb08922b0bd812a9, https://usegalaxy.org.au/published/workflow?id=2436bc493e76f438, https://usegalaxy.org.au/published/workflow?id=31a664d151978dc6, https://usegalaxy.org.au/published/workflow?id=481c666fbc7ffa02, https://usegalaxy.org.au/published/workflow?id=51aaafbd00b91717, https://usegalaxy.org.au/published/workflow?id=579da54989f5d55c, https://usegalaxy.org.au/published/workflow?id=5e3ff382ab802baf, https://usegalaxy.org.au/published/workflow?id=ac4799c5009f98d3, https://usegalaxy.org.au/published/workflow?id=b73280eaeb77a0a9, https://usegalaxy.org.au/published/workflow?id=d01ff75a4943fa79, https://usegalaxy.org.au/published/workflow?id=d6521e6c247eeaaf, https://usegalaxy.org.au/published/workflow?id=ecafc3d43b4c63f7, https://usegalaxy.org.au/published/workflow?id=ffeef94c4539c3e5, https://usegalaxy.org/published/workflow?id=0f6bb7847f8769af, https://usegalaxy.org/published/workflow?id=1a08efa0bf83d225, https://usegalaxy.org/published/workflow?id=3d0f92e7f63978b6, https://usegalaxy.org/published/workflow?id=6cad14c78ec330ac, https://usegalaxy.org/published/workflow?id=6f1da4e0830e6051, https://usegalaxy.org/published/workflow?id=84112c29ee53a5db, https://usegalaxy.org/published/workflow?id=92b67534076ae889, https://usegalaxy.org/published/workflow?id=a8fa62e35610d85e, https://usegalaxy.org/published/workflow?id=e3366346808b1f55, https://usegalaxy.org/published/workflow?id=ebdf324634e7243c, https://usegalaxy.org/published/workflow?id=fd511165e30cb62c, https://usegalaxy.org/published/workflow?id=fda56c998bb88e2a, https://usegalaxy.org/published/workflow?id=ff84d87fd3638a3f, https://workflowhub.eu/workflows/615?version=6
barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. 2017-08-25 https://github.com/tseemann/barrnap 1.2.2 barrnap 0.9 To update Sequence Analysis Gene prediction Gene prediction Genomics, Model organisms, Model organisms Genomics, Model organisms, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 719 719 11908 11908 0 0 0 0 281 417 7921 9428 21 21 420 420 21756 20249 1157 1021 https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=fe43cf59e48bf556
basil basil Breakpoint detection, including large insertions 2019-05-22 https://github.com/seqan/anise_basil 1.2.0 anise_basil 1.2.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 94 106 253 368 114 121 471 516 0 0 0 0 0 0 0 0 884 724 227 208 https://usegalaxy.org/published/workflow?id=e67b6da41e1e6932
bax2bam bax2bam BAX to BAM converter 2019-10-12 https://github.com/pacificbiosciences/bax2bam/ 0.0.11 bax2bam 0.0.11 Up-to-date Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 26 28 208 29 32 124 213 0 0 0 0 0 0 0 0 421 152 58 45
bayescan BayeScan Detecting natural selection from population-based genetic data 2017-03-09 http://cmpg.unibe.ch/software/BayeScan/index.html 2.1 bayescan 2.0.1 To update Sequence Analysis Statistical inference Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 35 109 136 0 0 0 0 0 0 0 0 0 0 0 0 136 109 35 28
bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. 2024-06-14 https://www.encodeproject.org/software/bedgraphtobigwig/ 0.1 ucsc-bedgraphtobigwig 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 71 339 339 204 204 1348 1348 0 0 0 0 0 0 0 0 1687 1687 275 275 https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656 epigenetics/formation_of_super-structures_on_xi
bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.37 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools bbmap BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. 6 3 6 6 0 0 0 0 0 0 0 0 0 0 1 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 413 413 25287 25287 562 562 10487 10487 172 172 3537 3537 5 5 134 134 39445 39445 1152 1152 https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/519?version=1
bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers 2015-08-12 https://samtools.github.io/bcftools/ 1.15.1 bcftools 1.22 To update Variant Analysis Data handling, Variant calling Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment DNA polymorphism, GWAS study, Genotyping experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 2017-10-05 https://github.com/dmaticzka/bctools 0.2.2 bctools 0.2.2 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 124 157 1759 3227 0 0 0 0 0 0 0 0 0 0 0 0 3227 1759 157 124 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://workflowhub.eu/workflows/1706?version=1 transcriptomics/clipseq
beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). 2023-08-11 https://github.com/EGA-archive/beacon2-ri-tools/tree/main 2.0.0 beacon2-ri-tools 2.0.5 To update Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 64 64 0 0 0 0 2 2 37 37 1 1 2 2 103 103 16 16
beagle beagle Beagle is a program for phasing and imputing missing genotypes. 2021-07-03 https://faculty.washington.edu/browning/beagle/beagle.html 5.4_29Oct24.c8e beagle 5.4_22Jul22.46e To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 252 252 0 0 0 0 0 0 0 0 2 2 4 4 256 256 45 45 https://usegalaxy.fr/published/workflow?id=4ec0bc782472fa10
bedops_sortbed bedops-sort-bed BEDOPS: high-performance genomic feature operations 2023-08-08 https://bedops.readthedocs.io/en/latest/ 2.4.42 bedops 2.4.42 Up-to-date Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 95 95 277 277 116 116 451 451 0 0 0 0 0 0 0 0 728 728 211 211
bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic 2014-09-13 https://github.com/arq5x/bedtools2 2.31.1 bedtools 2.31.1 Up-to-date Genomic Interval Operations, Text Manipulation Mapping Mapping Genomics Genomics iuc 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bellavista bellavista_prepare Open-Source Visualization for Imaging-Based Spatial Transcriptomics 2025-05-02 https://github.com/pkosurilab/BellaVista 0.0.2 To update Single Cell, Spatial Omics, Transcriptomics, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellavista https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellavista 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2
bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. 2021-05-28 https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 350 350 2265 2265 110 110 1644 1644 41 41 843 843 0 0 0 0 4752 4752 501 501 https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://usegalaxy.org/published/workflow?id=f09033420c6267ab, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/702?version=1 assembly/ERGA-post-assembly-QC, assembly/vgp_genome_assembly
berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. 2019-03-08 https://github.com/tseemann/berokka 0.2.3 berokka 0.2.3 Up-to-date Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 85 1250 1250 0 0 0 0 1250 1250 85 85
biapy biapy Accessible deep learning workflows on bioimages using BiaPy 2025-07-23 https://biapyx.github.io/ 3.6.5 python To update Machine Learning, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF 2024-02-18 https://github.com/medema-group/BiG-SCAPE 1.1.9 bigscape 2.0.0 To update Metagenomics Clustering, Global alignment, Fold recognition Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 2449 2449 0 0 0 0 0 0 0 0 0 0 0 0 2449 2449 95 95
bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files 2024-07-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed 0.2.4 python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 912 912 54 54 867 867 0 0 0 0 0 0 0 0 1779 1779 73 73 https://usegalaxy.eu/published/workflow?id=3b94f511c52da835
binette binette Binning refinement tool 2025-01-14 https://github.com/genotoul-bioinfo/Binette 1.1.2 binette 1.1.2 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette binette Binette Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 359 359 8 8 17 17 0 0 0 0 1 1 49 49 425 425 20 20 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=3
binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 236 236 0 0 0 0 0 0 0 0 0 0 0 0 236 236 64 64
bio_hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation 2017-09-29 https://github.com/phac-nml/bio_hansel 2.6.1 bio_hansel 2.6.1 Up-to-date Sequence Analysis Genotyping, SNP detection, Genome assembly Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 36 39 312 397 57 63 538 592 0 0 0 0 0 0 0 0 989 850 102 93
bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! 2016-11-03 https://github.com/veg/BioExt 0.21.10 python-bioext 0.21.10 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 833 833 33209 33209 1366 1366 22291 22291 1 1 2 2 0 0 0 0 55502 55502 2200 2200 https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=c03c18813a3380b3
bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics 2023-01-25 https://github.com/dariober/bioinformatics-cafe/ 0.1.0 python To update Sequence Analysis mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 130 130 1691 1691 126 126 1430 1430 0 0 0 0 0 0 0 0 3121 3121 256 256 https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539 variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2-variant-discovery
biomformat biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.15 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format biomformat biomformat This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 356 16688 16852 374 593 2736 5533 166 235 2283 2833 0 0 0 0 25218 21707 1184 882 https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/142?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 microbiome/mgnify-amplicon
biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. 2020-01-17 https://www.sanger.ac.uk/science/tools/bio-tradis 1.4.5 biotradis 1.4.5 Up-to-date Genome annotation Sequence analysis Sequence analysis Mobile genetic elements, Workflows Mobile genetic elements, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 165 176 6369 6769 0 0 0 0 0 0 0 0 6769 6369 176 165
biscot biscot Bionano scaffolding correction tool 2023-01-06 https://github.com/institut-de-genomique/biscot 2.3.3 biscot 2.3.3 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2
blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 121 128 908 952 69 77 156 193 18 18 185 185 0 0 0 0 1330 1249 223 208 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6
bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment 2017-05-08 http://bowtie-bio.sourceforge.net/bowtie2 2.5.4 bowtie2 2.5.4 Up-to-date Next Gen Mappers Read mapping Read mapping Mapping, Genomics, Mapping Mapping, Genomics, Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. 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bp_genbank2gff3 bp_genbank2gff3 Converts GenBank format files to GFF3 2015-08-14 https://bioperl.org/ 1.1 perl-bioperl 1.7.8 To update Sequence Analysis Data handling, Service invocation Data handling, Service invocation Genomics, Software engineering, Data management Genomics, Software engineering iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 638 721 10572 11606 974 1075 10887 11385 180 207 8997 9165 22 22 309 309 32465 30765 2025 1814 genome-annotation/secondary-metabolite-discovery
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bwa_mem2 bwa_mem2_idx, bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. 2021-10-08 https://github.com/bwa-mem2/bwa-mem2 2.3 bwa-mem2 2.3 Up-to-date Next Gen Mappers Sequence alignment Sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. 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bwameth bwameth Fast and accurate alignment of BS-seq reads 2016-09-14 https://github.com/brentp/bwa-meth 0.2.9 bwameth 0.2.9 Up-to-date Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 691 1020 10937 16134 862 907 12645 13009 176 176 1696 1700 2 2 2 2 30845 25280 2105 1731 https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1566?version=1 epigenetics/methylation-seq
cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program 2022-01-28 https://github.com/ComparativeGenomicsToolkit/cactus 2.7.1 To update Sequence Analysis Multiple sequence alignment, Genome alignment Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics Genomics, Sequence assembly, Mapping, Phylogenetics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 92 92 575 575 0 0 0 0 96 96 2883 2883 4 4 12 12 3470 3470 192 192
calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. 2019-08-26 https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold 1.0.0 numpy To update Visualization, Genomic Interval Operations, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. 2021-05-04 0.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 2700 2700 7 7 379 379 0 0 0 0 0 0 0 0 3079 3079 28 28 https://usegalaxy.eu/published/workflow?id=40d2c7ac42bd5302, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1876?version=1
cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments 2024-05-20 https://github.com/CAMI-challenge/AMBER 2.0.7 cami-amber 2.0.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber cami-amber AMBER AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 10522 10522 0 0 0 0 0 0 0 0 0 0 0 0 10522 10522 8 8 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1
cawlign cawlign Codon-aware alignment of sequences to a reference. 2025-09-30 https://github.com/veg/cawlign 0.1.14 cawlign 0.1.14 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign https://github.com/galaxyproject/tools-iuc/tree/main/tools/cawlign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cd_hit cd_hit Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 899 899 20148 20148 1 1 2 2 1 1 2 2 57 57 1174 1174 21326 21326 958 958 https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5
cemitool cemitool Gene co-expression network analysis tool 2022-10-10 https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html 1.30.0 bioconductor-cemitool 1.30.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Pathway or network analysis Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 354 354 87 87 584 584 6 6 154 154 0 0 0 0 1092 1092 138 138
charts charts Enables advanced visualization options in Galaxy Charts 2018-01-30 https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2016 2636 4166 5631 3945 8272 8242 16754 8 145 13 350 58 58 111 111 22846 12532 11111 6027 https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org/published/workflow?id=cb03300161109123
checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes 2022-07-29 https://github.com/Ecogenomics/CheckM 1.2.4 checkm-genome 1.2.4 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 717 717 12189 12189 179 179 1510 1510 96 96 2254 2254 50 50 1469 1469 17422 17422 1042 1042 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=3 microbiome/metagenomics-binning
checkm2 checkm2 Rapid assessment of genome bin quality using machine learning 2024-11-08 https://github.com/chklovski/CheckM2 1.1.0 checkm2 1.1.0 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 1602 1602 187 187 1322 1322 0 0 0 0 15 15 1268 1268 4192 4192 430 430 https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1882?version=2 genome-annotation/bacterial-genome-quality-control
cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions 2022-12-09 https://github.com/BackofenLab/Cherri 0.7 cherri 0.8 To update Transcriptomics, RNA Molecular interactions, pathways and networks, Structure analysis, Machine learning Molecular interactions, pathways and networks, Structure analysis, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 1 207 207 0 0 0 0 0 0 0 0 0 0 0 0 207 207 1 1
chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm 2024-04-13 https://github.com/B-UMMI/chewBBACA/tree/master chewbbaca 3.4.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 100 9644 9644 0 0 0 0 0 0 0 0 0 0 0 0 9644 9644 100 100
chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data 2020-01-19 https://github.com/pavanvidem/chira 1.4.3 chira 1.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 128 137 39830 42352 95 95 21742 21742 17 17 585 585 0 0 0 0 64679 62157 249 240 https://usegalaxy.eu/published/workflow?id=25a209bda998412f, https://usegalaxy.eu/published/workflow?id=26c4882e320ed7b3, https://usegalaxy.eu/published/workflow?id=66834f10c86362b9, https://workflowhub.eu/workflows/1681?version=1, https://workflowhub.eu/workflows/66?version=1, https://workflowhub.eu/workflows/67?version=1 transcriptomics/rna-interactome
chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing 2023-01-18 https://github.com/cumbof/chopin2 1.0.9.post1 chopin2 To update Machine Learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 21 21 0 0 0 0 0 0 0 0 21 21 8 8 statistics/hyperdimensional_computing
chopper chopper Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT. 2025-07-22 https://github.com/wdecoster/chopper 0.11.0 chopper 0.11.0 Up-to-date Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 6 6 https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67
chromeister chromeister ultra-fast pairwise genome comparisons 2020-09-30 https://github.com/estebanpw/chromeister 1.5.a chromeister 1.5.a Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 550 550 10141 10141 0 0 0 0 277 277 1883 1883 56 56 2443 2443 14467 14467 883 883 https://usegalaxy.org.au/published/workflow?id=478c79365fc9677f, https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489, https://usegalaxy.org.au/published/workflow?id=d06665e4bc7fff6d, https://usegalaxy.org.au/published/workflow?id=d957bfeb3cd03db0, https://workflowhub.eu/workflows/1545?version=1, https://workflowhub.eu/workflows/1646?version=1 assembly/assembly-quality-control, genome-annotation/hpc-for-lsgc
cialign cialign Tool to clean, visualise and analyse a multiple sequence alignment 2025-08-04 https://github.com/KatyBrown/CIAlign 1.1.4 cialign 1.1.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 3 3
circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. 2022-08-26 https://github.com/YangLab/CIRCexplorer2 2.3.8 circexplorer2 2.3.8 Up-to-date RNA, Assembly RNA splicing, Gene transcripts, Literature and language RNA splicing, Gene transcripts, Literature and language iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 833 833 0 0 0 0 0 0 0 0 0 0 0 0 833 833 39 39
circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy 2017-08-07 http://circos.ca/ 0.69.8 circos 0.69.9 To update Graphics Sequence visualisation Sequence visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. 11 11 11 11 0 0 0 0 0 0 0 0 0 0 11 11 11 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 1387 1476 30286 32934 1656 1808 33780 36943 409 515 10963 28143 24 25 586 588 98608 75615 3824 3476 https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=75e88603745e069e, https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.org.au/published/workflow?id=0f9a29e8eac2075c, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=6588e175004aba38, https://usegalaxy.org.au/published/workflow?id=6a58898d37da5c83, https://usegalaxy.org.au/published/workflow?id=f85353f93461d180, https://workflowhub.eu/workflows/1413?version=1, https://workflowhub.eu/workflows/1415?version=1, https://workflowhub.eu/workflows/1419?version=1, https://workflowhub.eu/workflows/1651?version=1, https://workflowhub.eu/workflows/676?version=1 assembly/ecoli_comparison, variant-analysis/somatic-variant-discovery, visualisation/circos, visualisation/circos-microbial
cite_seq_count cite_seq_count Count CMO/HTO 2023-01-18 https://github.com/Hoohm/CITE-seq-Count 1.4.4 cite-seq-count 1.4.5 To update Single Cell, Transcriptomics, Proteomics RNA-Seq quantification RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Transcriptomics, Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 23 23 6 6 21 21 1 1 290 290 0 0 0 0 334 334 12 12 https://usegalaxy.eu/published/workflow?id=4cb8f782994763a4, https://usegalaxy.eu/published/workflow?id=5009d8d7a907a825, https://usegalaxy.eu/published/workflow?id=6ed089fe65347272, https://usegalaxy.eu/published/workflow?id=865715636d40b798, https://usegalaxy.eu/published/workflow?id=a18615f77ed3f371, https://usegalaxy.eu/published/workflow?id=a72e3cb6eb656102, https://usegalaxy.eu/published/workflow?id=c4327bccfa623f7e, https://usegalaxy.eu/published/workflow?id=e296e4ac941bf0de, https://usegalaxy.org.au/published/workflow?id=0f01e24e6c33a834, https://usegalaxy.org.au/published/workflow?id=109f0c68e617e104, https://usegalaxy.org.au/published/workflow?id=aa387984ac9e2f71, https://usegalaxy.org.au/published/workflow?id=b09530351a9e9ffb, https://usegalaxy.org.au/published/workflow?id=b88036506d0be117, https://usegalaxy.org.au/published/workflow?id=bcdbefda8e15e547, https://usegalaxy.org.au/published/workflow?id=d66f1a1c1ffd6275, https://usegalaxy.org/published/workflow?id=1d19cf599e1d4a0f, https://usegalaxy.org/published/workflow?id=3b88ab63573edb0f, https://usegalaxy.org/published/workflow?id=41c40e7aa6b24f51, https://usegalaxy.org/published/workflow?id=586b923221fb5da4, https://usegalaxy.org/published/workflow?id=73a8b48cbd6f1d8c, https://usegalaxy.org/published/workflow?id=90ac9dc2bd9d8092, https://usegalaxy.org/published/workflow?id=a737766dd083b280, https://workflowhub.eu/workflows/694?version=8
clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 1.0.10 clair3 1.2.0 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 328 328 5269 5269 52 52 1858 1858 13 13 246 246 2 2 54 54 7427 7427 395 395 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data
clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2268 2506 114395 117339 3966 8263 54653 99642 837 966 11073 13924 42 43 726 730 231635 180847 11778 7113 https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=a484a1e1a7335696, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1541?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data
clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy 2024-08-08 https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ 1.1.1 python To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 69 69 305 305 0 0 0 0 0 0 0 0 0 0 0 0 305 305 69 69 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6 evolution/mtb_transmission
cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 2.0.0 cnv-vcf2json To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 69 69 0 0 0 0 1 1 12 12 0 0 0 0 81 81 12 12 https://usegalaxy.eu/published/workflow?id=07b440eec3ac7c2e variant-analysis/beaconise_1000hg
cnv_phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 1.0.2 cnv-phenopacket To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 7 7 variant-analysis/beaconise_1000hg
cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_export_bed, cnvkit_breaks, cnvkit_call, cnvkit_export_cdt, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_export_jtv, cnvkit_export_nexus_basic, cnvkit_export_nexus_ogt, cnvkit_reference, cnvkit_scatter, cnvkit_export_seg, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target, cnvkit_theta, cnvkit_export_vcf detecting copy number variants and alterations genome-wide from high-throughput sequencing 2023-03-14 https://github.com/etal/cnvkit 0.9.12 cnvkit 0.9.12 Up-to-date Variant Analysis Variant calling Variant calling DNA structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. 0 25 25 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 59 59 3401 3401 0 0 0 0 3 3 430 430 0 0 0 0 3831 3831 62 62 https://usegalaxy.eu/published/workflow?id=07b440eec3ac7c2e
codeml codeml Detects positive selection 2017-07-19 http://abacus.gene.ucl.ac.uk/software/paml.html 4.9 paml 4.10.9 To update Phylogenetics Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Probabilistic sequence generation Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 72 84 62891 63000 0 0 0 0 0 0 0 0 0 0 0 0 63000 62891 84 72
cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons 2022-08-11 https://github.com/cbg-ethz/cojac 0.9.3 cojac 0.9.3 Up-to-date Metagenomics, Sequence Analysis Genetic variation Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 2763 2763 7 7 20 20 0 0 0 0 0 0 0 0 2783 2783 20 20 https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b
colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 2024-03-24 https://github.com/sokrypton/ColabFold 1.5.5 To update Proteomics, Graphics Database search, Protein structure prediction, Fold recognition Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 233 233 10606 10606 0 0 0 0 0 0 0 0 10606 10606 233 233
colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome 2017-10-02 https://colibread.inria.fr/ 24.7.14 commet 24.7.14 Up-to-date Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 52 1393 1457 0 0 0 0 0 0 0 0 68 68 259 262 1719 1652 120 115
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transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways, variant-analysis/pox-tiled-amplicon
column_order_header_sort column_order_header_sort Sort Column Order by heading 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 291 369 4668 5579 342 434 1768 2044 0 0 0 0 13 13 21 21 7644 6457 816 646 https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8
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comebin comebin Binning of metagenomic contigs using COntrastive Multi-viEw representation learning 2025-07-03 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1
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compress_file compress_file Compress files. 2022-02-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file 0.1.0 gzip To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 439 439 10916 10916 523 523 7826 7826 101 101 13887 13887 0 0 0 0 32629 32629 1063 1063 https://usegalaxy.eu/published/workflow?id=2062c7e1c50b05f3, https://usegalaxy.eu/published/workflow?id=32a0c4bbe6f9add9, https://usegalaxy.eu/published/workflow?id=c0c8228673b7191f, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.eu/published/workflow?id=e71ae1076d5f0584, https://usegalaxy.org.au/published/workflow?id=2f49a0a03d99c57a, https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf, https://usegalaxy.org.au/published/workflow?id=8004dce1906ec057, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=fc74419b109527b2, https://usegalaxy.org/published/workflow?id=40be58638e230ab5, https://usegalaxy.org/published/workflow?id=5f621330d6339655, https://usegalaxy.org/published/workflow?id=67b9046dc5dbc009, https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae, https://workflowhub.eu/workflows/1648?version=1, https://workflowhub.eu/workflows/738?version=4 assembly/mitochondrion-assembly
concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. 2022-02-18 https://github.com/BinPro/CONCOCT 1.1.0 concoct 1.1.0 Up-to-date Metagenomics Sequence clustering, Read binning Sequence clustering, Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 107 107 9955 9955 19 19 187 187 0 0 0 0 4 4 3085 3085 13227 13227 130 130 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=58f779d238d569dc, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3
constava constava Calculate 'conformational states probabilities' and 'conformational state variability' from a protein structure ensemble 2024-08-13 https://github.com/bio2byte/constava 1.1.0 constava 1.1.0 Up-to-date Statistics, Proteomics Protein geometry calculation Protein geometry calculation Protein folding, stability and design Protein folding, stability and design iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava constava Constava Constava calculates conformational states probability and conformational state variability from protein structure ensembles. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
contig_annotation_tool cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) 2019-11-27 https://github.com/dutilh/CAT 5.2.3 cat 6.0.1 To update Metagenomics Taxonomic classification, Sequence assembly, Coding region prediction Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. 5 2 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 257 267 17418 17676 216 231 1590 1750 84 85 848 875 0 0 0 0 20301 19856 583 557 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef
control_freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. 2020-07-22 http://boevalab.inf.ethz.ch/FREEC/ 11.6 gawk To update Variant Analysis Copy number estimation, Variant calling, Genome alignment Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining Oncology, Human genetics, Data mining iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 118 118 1565 1575 0 0 0 0 4 4 201 201 1 1 17 17 1793 1783 123 123 https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=75e88603745e069e, https://usegalaxy.eu/published/workflow?id=7cc253b53379b727, https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1, https://workflowhub.eu/workflows/1651?version=1, https://workflowhub.eu/workflows/676?version=1 variant-analysis/somatic-variant-discovery
coreprofiler coreprofiler_allele_calling CoreProfiler, a tool for cgMLST allele calling from bacterial genome assemblies 2025-07-22 https://gitlab.com/ifb-elixirfr/abromics/coreprofiler 1.1.6 coreprofiler 1.1.6 Up-to-date Variant Analysis Multilocus sequence typing Multilocus sequence typing Microbiology, Bioinformatics, Phylogenetics Microbiology, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler coreprofiler CoreProfiler CoreProfiler is a cgMLST (core genome multilocus sequence typing) software that identifies alleles in bacterial genome assemblies by comparing them to a reference allele scheme. It detects both exact matches to known alleles and potential novel alleles using a two-step BLAST-based approach, enabling robust and reproducible strain genotyping. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cosg cosg Marker gene identification for single-cell sequencing data using COSG. 2024-05-29 https://github.com/genecell/COSG 1.0.1 cosg 1.0.3 To update Transcriptomics, Sequence Analysis, Single Cell Nucleic acid sequence analysis Nucleic acid sequence analysis Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg cosg COSG COSG is a cosine similarity-based method for more accurate and scalable marker gene identification. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://usegalaxy.eu/published/workflow?id=9adf0402b641042c
coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file 2017-10-16 https://github.com/galaxyproject/tools-iuc 0.0.4 perl-number-format 1.76 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coverm coverm_contig, coverm_genome CoverM genome and contig wrappers 2022-04-26 https://github.com/wwood/CoverM 0.7.0 coverm 0.7.0 Up-to-date Sequence Analysis Local alignment Local alignment Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm coverm CoverM Read coverage calculator for metagenomics 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 147 147 3594 3594 14 14 414 414 11 11 125 125 7 7 565 565 4698 4698 179 179 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
cramino cramino A tool for quick quality assessment of cram and bam files, intended for long read sequencing. 2025-06-17 https://github.com/wdecoster/cramino 1.1.0 cramino 1.1.0 Up-to-date Statistics, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cramino https://github.com/galaxyproject/tools-iuc/tree/main/tools/cramino 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. 2019-08-13 https://github.com/moineaulab/CRISPRStudio 1+galaxy0 crispr_studio 1 To update Sequence Analysis Visualisation Visualisation Sequence analysis, Genomics, Data visualisation Sequence analysis, Genomics, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 94 103 2795 2880 0 0 0 0 0 0 0 0 0 0 0 0 2880 2795 103 94
crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool 2018-07-27 https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 To update Transcriptomics, Visualization, Single Cell Filtering, Sequence contamination filtering, Sequencing quality control, RNA-Seq analysis Filtering, Sequence contamination filtering, RNA-Seq analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter cross-contamination_barcode_filter Cross-contamination Barcode Filter This tool produces plots enabling the discovery of cross-contamination of samples across the full selection of barcodes used in a sequencing plate. It also filters false barcodes from each batch and retains only the 'real' barcodes. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 68 99 146 415 48 49 82 144 0 0 0 0 0 0 0 0 559 228 148 116
crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies 2016-04-04 http://crossmap.sourceforge.net/ 0.7.3 crossmap 0.7.3 Up-to-date Convert Formats, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 84 104 2277 2776 222 254 4500 5654 0 0 0 0 0 0 0 0 8430 6777 358 306
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cuffnorm cuffnorm The Cuffnorm tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 66 117 302 707 202 1179 713 13525 49 71 287 367 0 0 0 0 14599 1302 1367 317
cuffquant cuffquant The Cuffquant tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 49 79 352 767 192 1326 1070 15964 22 47 257 426 0 0 0 0 17157 1679 1452 263 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.org/published/workflow?id=8b2c8c8ce121177d, https://workflowhub.eu/workflows/40?version=1
cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). 2018-02-20 https://cutadapt.readthedocs.org/en/stable/ 5.1 cutadapt 5.1 Up-to-date Fasta Manipulation, Fastq Manipulation, Sequence Analysis Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Genomics, Probes and primers, Sequencing lparsons https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14131 16253 330892 364942 22476 26008 409500 482165 4256 4631 79748 86014 1579 1582 59464 59550 992671 879604 48474 42442 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cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. 2020-09-23 https://github.com/tjiangHIT/cuteSV 2.1.3 cutesv 2.1.3 Up-to-date Variant Analysis Split read mapping, Genotyping, Structural variation detection Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Sequencing, Computer science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 58 58 344 344 0 0 0 0 11 11 166 166 0 0 0 0 510 510 69 69
cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. 2015-12-18 1.1.1 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 85 60 283 0 0 0 0 0 0 0 0 283 60 85 33
dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers 2019-07-05 https://benjjneb.github.io/dada2/index.html 1.34.0 bioconductor-dada2 1.34.0 Up-to-date Metagenomics Variant calling, DNA barcoding Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics Sequencing, Genetic variation, Microbial ecology, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. 10 10 11 11 0 0 0 0 0 0 0 0 0 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 10 0 865 885 205808 209081 1301 1344 254475 270135 179 179 52639 52639 72 72 38131 38131 569986 551053 2480 2417 https://usegalaxy.eu/published/workflow?id=48d0dc424e71d8c2, https://usegalaxy.eu/published/workflow?id=642f4c47028031d7, https://usegalaxy.eu/published/workflow?id=7b557efda89bb998, https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372, https://usegalaxy.eu/published/workflow?id=e132370adf8f2838, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.fr/published/workflow?id=b5d86d505c09d170, https://usegalaxy.org.au/published/workflow?id=1016f17b77a8216d, https://usegalaxy.org.au/published/workflow?id=2d05f15a9616cc47, https://usegalaxy.org.au/published/workflow?id=400fbd96fb04c60e, https://usegalaxy.org/published/workflow?id=0942f2f3386e6b41, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://usegalaxy.org/published/workflow?id=5df593510c7d944d, https://usegalaxy.org/published/workflow?id=78e60413358273bc, https://usegalaxy.org/published/workflow?id=806ef8816168916f, https://usegalaxy.org/published/workflow?id=e067c4e66f0af362, https://usegalaxy.org/published/workflow?id=ecf3a7f9da7409ef, https://workflowhub.eu/workflows/1395?version=2, https://workflowhub.eu/workflows/790?version=3 microbiome/dada-16S
das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics 2022-06-23 https://github.com/cmks/DAS_Tool 1.1.7 das_tool 1.1.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 77 77 6906 6906 12 12 283 283 0 0 0 0 3 3 1185 1185 8374 8374 92 92 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3
data_manager_homer_preparse homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. 2021-08-08 http://homer.ucsd.edu/homer/index.html 4.11 homer 5.1 To update Sequence Analysis Sequence motif discovery Sequence motif discovery iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 293 293 11363 11363 0 0 0 0 0 0 0 0 23 24 388 534 11897 11751 317 316 https://usegalaxy.eu/published/workflow?id=d3a4e6cc1b4565e5
data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool 2016-02-18 1.0.0 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. 2015-08-03 https://www.gnu.org/software/datamash/ 1.9 datamash 1.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 3 3 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 6000 6432 876492 892401 5184 5885 114632 134970 2485 2521 24641 25144 249 250 5920 5956 1058471 1021685 15088 13918 https://usegalaxy.cz/published/workflow?id=a5241f01bb65bd38, https://usegalaxy.eu/published/workflow?id=030e978022e19375, 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statistics/flexynesis_survival, transcriptomics/rna-seq-viz-with-heatmap2, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2-variant-discovery
decontam decontam Removes decontamination features (ASVs/OTUs) using control samples 2024-09-13 https://github.com/benjjneb/decontam 1.22.0 bioconductor-decontam 1.26.0 To update Metagenomics Classification Classification Metagenomics, Microbial ecology, Sequencing Metagenomics, Microbial ecology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 32 32 0 0 0 0 0 0 0 0 0 0 0 0 32 32 8 8 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264
decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data 2023-01-09 https://github.com/cbib/decontaminator 1.0.0 numpy To update Machine Learning Filtering Filtering Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 41 41 349 349 0 0 0 0 0 0 0 0 0 0 0 0 349 349 41 41
deeparg deeparg_predict, deeparg_short_reads A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes 2024-10-07 https://github.com/gaarangoa/deeparg 1.0.4 deeparg 1.0.4 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Antimicrobial resistance prediction Antimicrobial resistance prediction, Antimicrobial resistance prediction Microbiology Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg deeparg DeepARG A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 20 108 108 0 0 0 0 0 0 0 0 4 4 65 65 173 173 24 24
deepmicro deepmicro Representation learning and classification framework 2023-03-16 https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 Up-to-date Machine Learning Essential dynamics, Splitting, Community profiling Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 560 560 0 0 0 0 0 0 0 0 0 0 0 0 560 560 9 9
deepsig deepsig Predictor of signal peptides in proteins based on deep learning 2023-04-28 https://github.com/BolognaBiocomp/deepsig 1.2.5 deepsig 1.2.5 Up-to-date Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 131 131 388 388 0 0 0 0 0 0 0 0 11 11 45 45 433 433 142 142 https://usegalaxy.eu/published/workflow?id=a018307be3563f28
deepvariant deepvariant DeepVariant is a deep learning-based variant caller 2021-09-06 https://github.com/google/deepvariant 1.5.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 546 546 5121 5121 789 789 6696 6696 0 0 0 0 0 0 0 0 11817 11817 1335 1335 https://usegalaxy.org/published/workflow?id=39753cc73284963f, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e7586d70715207b5
deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables 2018-11-22 https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0+galaxy1 bedtools 2.31.1 To update Transcriptomics, Single Cell RNA-Seq analysis, Gene functional annotation RNA-Seq analysis, Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate deg_annotate DEG Annotate This tool appends the output table of DESeq2 or DEXSeq with gene symbols, biotypes, positions etc. The information you want to add is configurable. 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delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. 2020-09-28 https://github.com/dellytools/delly 0.9.1 delly 1.5.0 To update Variant Analysis Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis Indel detection, Structural variation detection, Genotyping DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 185 185 3117 3117 0 0 0 0 0 0 0 0 0 0 0 0 3117 3117 185 185
deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution 2014-12-03 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 2.11.40.8 bioconductor-deseq2 1.46.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis, RNA-Seq analysis Differential gene expression analysis, RNA-Seq analysis RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13707 15994 110682 133936 27214 37996 191581 286575 2980 3614 19899 24448 820 824 4511 4530 449489 326673 58428 44721 https://usegalaxy.eu/published/workflow?id=02a212cc9f134570, https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=0fa523529c4f73cf, https://usegalaxy.eu/published/workflow?id=12c80c5b5e2305d8, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=1fe02012c96b731f, https://usegalaxy.eu/published/workflow?id=1ffc058273ab357e, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=2287afbf248d9c89, https://usegalaxy.eu/published/workflow?id=250e6058f160825f, 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https://usegalaxy.org/published/workflow?id=eb01b539d17580c3, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=fb903de4aa4d5090, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1676?version=1, https://workflowhub.eu/workflows/1677?version=1, https://workflowhub.eu/workflows/1685?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/338?version=1, https://workflowhub.eu/workflows/412?version=1 transcriptomics/de-novo, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/srna
dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq 2015-09-25 https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html 1.48.0 bioconductor-dexseq 1.52.0 To update Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Exonic splicing enhancer prediction Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 274 481 14442 18733 646 1620 16356 30696 65 101 2756 4812 8 9 97 98 54339 33651 2211 993 https://usegalaxy.org/published/workflow?id=82681bd5f059e39a transcriptomics/ref-based
diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. 2021-03-21 https://github.com/bbuchfink/diamond 2.1.13 diamond 2.1.13 Up-to-date Sequence Analysis Sequence alignment analysis Sequence alignment analysis Sequence analysis, Proteins Sequence analysis, Proteins bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1620 1706 112648 114376 665 1048 35921 43599 446 448 65850 66062 125 125 2180 2208 226245 216599 3327 2856 https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ff4d5beb6ce1809d, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1641?version=1 assembly/ERGA-post-assembly-QC, genome-annotation/functional, genome-annotation/gene-centric, sequence-analysis/ncbi-blast-against-the-madland
diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. 2018-01-21 http://bioconductor.org/packages/release/bioc/html/DiffBind.html 3.12.0 bioconductor-diffbind 3.16.0 To update ChIP-seq Differential binding analysis Differential binding analysis ChIP-seq ChIP-seq bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 667 792 9452 11112 1268 2073 13935 20417 80 101 1868 2386 69 69 130 130 34045 25385 3035 2084 https://usegalaxy.eu/published/workflow?id=719314fa5263b501, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf
diffdock diffdock Diffusion Steps, Twists, and Turns for Molecular Docking. 2025-06-27 https://github.com/gcorso/DiffDock 1.1.3 To update Computational chemistry iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffdock https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffdock 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 6 6
dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. 2023-07-19 https://github.com/cbib/DIMet 0.2.4 dimet 0.2.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler 2017-10-26 http://disco.omicsbio.org/ disco 1.3 To update Metagenomics, Assembly Protein sequence analysis Protein sequence analysis Structure determination Structure determination iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 127 163 280 453 406 435 1525 1690 0 0 0 0 0 0 0 0 2143 1805 598 533
dnabot dnabot DNA assembly using BASIC on OpenTrons 2022-04-17 https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT 3.1.0 dnabot To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1576?version=1 synthetic-biology/basic_assembly_analysis
dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. 2022-12-08 https://github.com/Edinburgh-Genome-Foundry/DnaWeaver 1.0.2 dnaweaver_synbiocad 1.0.2 Up-to-date Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dos2unix dos2unix dos2unix convert text files with DOS or Mac line breaks to Unix line breaks and vice versa. 2025-07-11 https://waterlan.home.xs4all.nl/dos2unix.html 7.5.2 dos2unix To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dos2unix https://github.com/galaxyproject/tools-iuc/tree/main/tools/dos2unix 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 7 7
dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function 2022-09-01 https://github.com/WrightonLabCSU/DRAM 1.5.0 dram 1.5.0 Up-to-date Metagenomics Gene functional annotation Gene functional annotation Metagenomics, Biological databases, Molecular genetics Metagenomics, Biological databases, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 120 120 13633 13633 0 0 0 0 0 0 0 0 0 0 0 0 13633 13633 120 120
drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.6.2 drep 3.6.2 Up-to-date Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 113 115 1708 1749 13 13 47 47 0 0 0 0 38 38 1273 1273 3069 3028 166 164 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://workflowhub.eu/workflows/1352?version=3 genome-annotation/bacterial-genome-quality-control
dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data 2019-06-04 https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html 1.10.0 bioconductor-dropletutils 1.26.0 To update Single Cell, Sequence Analysis Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics Sequencing, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 450 517 4128 4902 381 385 5328 5345 42 46 2038 2190 34 34 110 110 12547 11604 982 907 https://usegalaxy.eu/published/workflow?id=0f563f176bb245af, https://usegalaxy.eu/published/workflow?id=3403d5a8a71e0c3c, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=6a6e2c2335051fb5, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=7d22eea4278570e8, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=90a32c95b60f5221, https://usegalaxy.eu/published/workflow?id=a1cfb476e849fce3, https://usegalaxy.eu/published/workflow?id=a3cb75fd31ba0689, https://usegalaxy.eu/published/workflow?id=af7c349497a75314, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d79309343e2a5d62, https://usegalaxy.eu/published/workflow?id=e7494f29c8672f34, https://usegalaxy.eu/published/workflow?id=e7a9e1a7728848cd, https://usegalaxy.eu/published/workflow?id=fa960b78dfc0c2f8, https://usegalaxy.eu/published/workflow?id=fd61d070d9744f95, https://usegalaxy.org.au/published/workflow?id=00da6615bca12a3c, https://usegalaxy.org.au/published/workflow?id=0458ecd2761307d1, https://usegalaxy.org.au/published/workflow?id=10296e860e9ef4bb, https://usegalaxy.org.au/published/workflow?id=281ea78467e73147, https://usegalaxy.org.au/published/workflow?id=3fd10af90a07f771, https://usegalaxy.org.au/published/workflow?id=41b115a9be4b6002, https://usegalaxy.org.au/published/workflow?id=471615c412b305f2, https://usegalaxy.org.au/published/workflow?id=644d8e4c78df8e36, https://usegalaxy.org.au/published/workflow?id=738350fc2ca69c0b, https://usegalaxy.org.au/published/workflow?id=c64dcc1e6a67f3e4, https://usegalaxy.org.au/published/workflow?id=f627023a3401bf9b, https://usegalaxy.org/published/workflow?id=4bbe4c8a6c52d03a, https://usegalaxy.org/published/workflow?id=516a2181b41af94e, https://usegalaxy.org/published/workflow?id=69712265fdb10ed5, https://usegalaxy.org/published/workflow?id=7aa36b1722ff4c11, https://usegalaxy.org/published/workflow?id=8e6d24a14d2908c2, https://usegalaxy.org/published/workflow?id=a6d6a2e8867fa566, https://usegalaxy.org/published/workflow?id=b73e416c06790ac5, https://usegalaxy.org/published/workflow?id=be7dab2274c1acdd, https://usegalaxy.org/published/workflow?id=cdb6c9c7037a95b2, https://workflowhub.eu/workflows/1523?version=1, https://workflowhub.eu/workflows/1527?version=1, https://workflowhub.eu/workflows/1546?version=1 single-cell/scrna-data-ingest, single-cell/scrna-preprocessing-tenx
drug2cell drug2cell Collection of utility functions for gene group activity evaluation in scanpy. 2025-01-21 https://github.com/Teichlab/drug2cell 0.1.2 drug2cell 0.1.2 Up-to-date Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/drug2cell https://github.com/galaxyproject/tools-iuc/tree/main/tools/drug2cell 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1
duplex_family_size_distribution fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families 2019-10-24 1.0.2 matplotlib To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 13 326 612 0 0 0 0 0 0 0 0 612 326 13 12
ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases 2016-11-29 http://www.ebi.ac.uk/services/all 0.1.1 six To update Web Services, Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 121 180 187 431 449 587 1055 1533 0 0 0 0 1 1 1 1 1965 1243 768 571
edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline 2017-09-11 http://bioconductor.org/packages/release/bioc/html/edgeR.html 3.36.0 bioconductor-edger 4.4.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq Genetics, RNA-Seq, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2767 3276 20681 25641 6109 8376 43822 64826 928 1075 7956 10252 29 30 172 173 100892 72631 12757 9833 https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org.au/published/workflow?id=0cfc1408fd9ea4e7, https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org.au/published/workflow?id=863eee1b041b6c58, https://usegalaxy.org/published/workflow?id=03258e0321162584, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=ce232859a466c75c, https://usegalaxy.org/published/workflow?id=d761637d43ee0324, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1556?version=1 single-cell/pseudobulk-analysis
ega_download_client pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. 2020-09-02 https://github.com/EGA-archive/ega-download-client 5.0.2 pyega3 5.2.0 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 138 2852 2852 55 55 208 208 5 5 459 459 0 0 0 0 3519 3519 198 198 https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://workflowhub.eu/workflows/1636?version=1, https://workflowhub.eu/workflows/363?version=2 variant-analysis/trio-analysis
egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing 2017-12-28 https://bioconductor.org/packages/release/bioc/html/EGSEA.html 1.20.0 bioconductor-egsea 1.34.0 To update Transcriptomics, RNA, Statistics, Single Cell Gene set testing Gene set testing Systems biology Systems biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 365 467 2481 3462 783 865 5041 5849 259 282 2025 2377 0 0 0 0 11688 9547 1614 1407 https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=8b1e2fe9f4a07de0, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://workflowhub.eu/workflows/1699?version=1 transcriptomics/rna-seq-genes-to-pathways
emboss emboss_needle, emboss_needleall Galaxy wrappers for EMBOSS6 tools 2025-01-17 http://emboss.open-bio.org/ 6.6.0 emboss 6.6.0 Up-to-date Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 419 419 0 0 0 0 0 0 0 0 0 0 0 0 419 419 62 62
emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools 2017-01-11 http://emboss.open-bio.org/ 5.0.0 emboss 6.6.0 To update Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 emboss EMBOSS Diverse suite of tools for sequence analysis; 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ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 2020-06-10 https://github.com/usegalaxy-eu/ena-upload-cli 0.9.0 ena-upload-cli 0.9.0 Up-to-date Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 48 48 418 418 0 0 0 0 15 15 1833 1833 0 0 0 0 2251 2251 63 63 https://usegalaxy.eu/published/workflow?id=924edc19e0653870, https://workflowhub.eu/workflows/1409?version=1 galaxy-interface/upload-data-to-ena
ena_webin_cli ena_webin_cli Submits a genome assembly to the European Nucleotide Archive (ENA) using the Webin-CLI Submission tool. 2025-02-27 https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html 9.0.1 ena-webin-cli 9.0.1 Up-to-date Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API 2017-08-05 https://github.com/bebatut/enasearch enasearch 0.2.2 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 161 221 1661 2454 0 0 0 0 0 0 0 0 0 0 0 0 2454 1661 221 161
ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions 2022-05-11 https://github.com/Ensembl/ensembl-vep 115.2 ensembl-vep 115.2 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 269 269 3860 3860 0 0 0 0 0 0 0 0 0 0 0 0 3860 3860 269 269 https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=99ad31bf3970ade4, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1
episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python 2023-03-13 https://github.com/colomemaria/epiScanpy 0.3.2 episcanpy 0.4.0 To update Single Cell, Epigenetics Enrichment analysis, Imputation Enrichment analysis, Imputation Epigenomics, Cell biology, DNA Epigenomics, Cell biology, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 53 53 1075 1075 53 53 406 406 2 2 766 766 0 0 0 0 2247 2247 108 108 https://workflowhub.eu/workflows/1502?version=1, https://workflowhub.eu/workflows/1506?version=1 single-cell/scatac-preprocessing-tenx
ete_treeviewer ete_treeviewer A toolkit for the analysis and visualization of trees. 2024-11-25 http://etetoolkit.org 3.1.3 curl To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 130 130 1626 1626 0 0 0 0 0 0 0 0 4 4 5 5 1631 1631 134 134 https://workflowhub.eu/workflows/1650?version=1 sequence-analysis/tapscan-streptophyte-algae
eukrep eukrep Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets 2025-07-30 https://github.com/patrickwest/EukRep 0.6.7 eukrep 0.6.7 Up-to-date Metagenomics Nucleic acid sequence analysis Nucleic acid sequence analysis Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep eukrep EukRep Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. 2024-07-19 https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file 2.1.0 evidencemodeler 2.1.0 Up-to-date Genome annotation Gene prediction Gene prediction Gene expression, Gene structure Gene expression, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 27 27 0 0 0 0 0 0 0 0 0 0 0 0 27 27 12 12
exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data 2019-11-08 https://cran.r-project.org/package=ExomeDepth 1.1.0 r-exomedepth 1.1.18 To update Sequence Analysis, Variant Analysis Sequence analysis, Variant calling, Genotyping, Copy number estimation Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 61 72 540 607 183 203 2916 3164 0 0 0 0 0 0 0 0 3771 3456 275 244
exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. 2018-08-02 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0 exonerate 2.4.0 Up-to-date Sequence Analysis Pairwise sequence alignment, Protein threading, Genome alignment Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 184 212 829 1242 191 222 733 1220 39 39 1230 1230 26 27 570 582 4274 3362 500 440
export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 2017-03-03 https://bitbucket.org/CibioCM/export2graphlan/overview 0.20 export2graphlan 0.22 To update Metagenomics Conversion Conversion Taxonomy, Metabolomics, Biomarkers Taxonomy, Metabolomics, Biomarkers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 589 710 6276 7303 193 213 712 791 122 123 616 632 16 16 43 43 8769 7647 1062 920 https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. 2016-01-14 3.0.3+galaxy3 bx-python 0.14.0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 1 1 0 0 0 0 0 0 1 1 1 0 930 1169 9749 15264 1876 12291 18355 263352 0 63 0 611 0 3 0 201 279428 28104 13526 2806 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=d3a8741131485af2, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.org/published/workflow?id=0ac68ec25f3534da, https://usegalaxy.org/published/workflow?id=28e86ab943c67417, https://usegalaxy.org/published/workflow?id=30507545aa971637, https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778, https://usegalaxy.org/published/workflow?id=4769befb88f653d6, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=6e75ac640853d0dd, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11, https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=94de815260acc3a8, https://usegalaxy.org/published/workflow?id=a666aaaa32f62487, https://usegalaxy.org/published/workflow?id=b8fdf05ec7540510, https://usegalaxy.org/published/workflow?id=ce2619816ce10220, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1706?version=1 epigenetics/cut_and_run, transcriptomics/clipseq
fairy fairy_cov, fairy_sketch Fast approximate contig coverage for metagenomic binning 2024-12-20 https://github.com/bluenote-1577/fairy 0.5.8 fairy 0.5.8 Up-to-date Metagenomics Read binning, Sequence assembly validation Read binning, Sequence assembly validation Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy fairy fairy fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. It can- Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)- Give comparable bins for multi-sample binning (short read or nanopore reads)- Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 148 148 0 0 0 0 0 0 0 0 0 0 0 0 148 148 5 5
falco falco A high throughput sequence QC analysis tool 2024-04-17 https://github.com/smithlabcode/falco/ 1.2.4 falco 1.2.5 To update Sequence Analysis Sequencing quality control, Visualisation, Read mapping Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Workflows, Mapping, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 3878 3878 162045 162045 965 965 16492 16492 274 274 5029 5029 24 24 357 357 183923 183923 5141 5141 https://usegalaxy.eu/published/workflow?id=259f459a45e17e46, https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=6368019ffdf6c5ee, https://usegalaxy.eu/published/workflow?id=8b8e89b9b8801f2f, https://usegalaxy.eu/published/workflow?id=b144287d56b3291b, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=7cd1acb1da823cdc, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/1845?version=1 assembly/mrsa-illumina, ecology/ENA_Biodiv_submission, epigenetics/cut_and_run, epigenetics/methylation-seq, galaxy-interface/workflow-fairification, sequence-analysis/quality-contamination-control, transcriptomics/mirna-target-finder, transcriptomics/ref-based, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants
fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 150 159 895 1011 262 287 1203 1346 0 0 0 0 2 2 2 2 2359 2100 448 414
fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 45 45 306 306 0 0 0 0 96 140 5703 6332 1 1 1 1 6639 6010 186 142
fasta_formatter cshl_fasta_formatter FASTA Width formatter 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 363 452 12086 12696 479 2140 4061 26449 76 107 733 1260 8 9 50 60 40465 16930 2708 926 https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a, https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=63db7f52a280bd2d, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=9bea2e9f45f07f32, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=a808c139402d7b87, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1738?version=1, https://workflowhub.eu/workflows/1739?version=1, https://workflowhub.eu/workflows/1740?version=1, https://workflowhub.eu/workflows/1741?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1 microbiome/mgnify-amplicon
fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74 125 383 882 207 747 1415 5767 18 24 427 550 6 8 20 31 7230 2245 904 305 https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d
fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. 2016-03-06 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot 1.0.1 openjdk To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 392 494 170 230 745 1074 0 0 0 0 0 0 0 0 1568 1137 295 225
fasta_stats fasta-stats Display summary statistics for a fasta file. 2018-11-21 https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3829 4225 56351 58340 4298 4623 34345 35598 2435 3021 17734 22805 147 147 749 749 117492 109179 12016 10709 https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.eu/published/workflow?id=9ddb703e1db13504, https://usegalaxy.eu/published/workflow?id=b1d9e56aef03672b, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=044b6b475b4db27a, https://usegalaxy.org.au/published/workflow?id=1ad4c47cee851dda, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=36604d0ab0dee988, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=5b32e2f0d390a4ba, https://usegalaxy.org.au/published/workflow?id=5cd804644a34c8fd, https://usegalaxy.org.au/published/workflow?id=68f5c371adbe5490, https://usegalaxy.org.au/published/workflow?id=705658f68ae73930, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=d832905fbaf2ca31, https://usegalaxy.org.au/published/workflow?id=df11f09771e73e04, https://usegalaxy.org.au/published/workflow?id=e5dfeff4a3068f36, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=f83a3cda33131fb8, https://usegalaxy.org/published/workflow?id=0602c14704dbe1ff, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://usegalaxy.org/published/workflow?id=c8d74054c1820087, https://usegalaxy.org/published/workflow?id=cdcf91a8ddb5dcd1, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://usegalaxy.org/published/workflow?id=de9c2db125a5ea27, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1509?version=1, https://workflowhub.eu/workflows/1549?version=1, https://workflowhub.eu/workflows/1578?version=1, https://workflowhub.eu/workflows/1595?version=1, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/1626?version=1, https://workflowhub.eu/workflows/221?version=3, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/226?version=1, https://workflowhub.eu/workflows/237?version=2, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/750?version=3, https://workflowhub.eu/workflows/794?version=2 assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/hifi-assembly, assembly/largegenome, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/braker3
fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1182 1205 29436 29626 1 1 18 18 133 133 1799 1799 64 64 949 949 32392 32202 1403 1380 https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75
fastk fastk_fastk, fastk_histex, fastk_logex FastK: A K-mer counter (for HQ assembly data sets) 2024-05-03 https://github.com/thegenemyers/FASTK 1.1.0 fastk 1.1.0 Up-to-date Assembly k-mer counting, Sequence analysis k-mer counting, Sequence analysis Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk fastk FASTK FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 46 46 742 742 45 45 389 389 0 0 0 0 0 0 0 0 1131 1131 91 91
fastp fastp Fast all-in-one preprocessing for FASTQ files 2018-03-07 https://github.com/OpenGene/fastp 1.0.1 fastp 1.0.1 Up-to-date Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. 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https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/1881?version=1, https://workflowhub.eu/workflows/224?version=1, https://workflowhub.eu/workflows/346?version=1, https://workflowhub.eu/workflows/353?version=1, https://workflowhub.eu/workflows/357?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1, https://workflowhub.eu/workflows/439?version=4, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/68?version=1 assembly/assembly-with-preprocessing, assembly/largegenome, assembly/mrsa-illumina, assembly/mrsa-nanopore, ecology/eDNA-taxonomic-analysis, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/beer-data-analysis, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/quality-contamination-control, transcriptomics/differential-isoform-expression, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2, variant-analysis/tb-variant-analysis
fastplong fastplong Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). 2025-05-06 https://github.com/OpenGene/fastplong 0.4.1 fastplong 0.4.1 Up-to-date Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 309 309 0 0 0 0 8 8 217 217 0 0 0 0 526 526 48 48 https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3
fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 241 306 9199 9921 880 3131 50082 77184 83 102 1967 2373 16 17 353 354 89832 61601 3556 1220 https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org/published/workflow?id=5b2a0da883be03b7, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395
fastq_dl fastq_dl Download FASTQ files from ENA. 2024-11-14 https://github.com/rpetit3/fastq-dl 3.0.1 fastq-dl 3.0.1 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 303 303 167 167 621 621 0 0 0 0 0 0 0 0 924 924 229 229 https://usegalaxy.eu/published/workflow?id=32219131f48494bf, https://usegalaxy.eu/published/workflow?id=c8d70d4402852fb5, https://usegalaxy.org/published/workflow?id=77de7101effbff3d, https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b, https://workflowhub.eu/workflows/1274?version=2, https://workflowhub.eu/workflows/1853?version=1 microbiome/mgnify-amplicon
fastq_filter fastq_filter Filter FASTQ reads by quality score and length 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 867 1046 22450 29161 2532 9682 35516 127334 219 331 4753 6800 84 84 436 436 163731 63155 11143 3702 https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.eu/published/workflow?id=e271d95a671182ec, https://usegalaxy.eu/published/workflow?id=f39528391f22aab0, https://usegalaxy.org.au/published/workflow?id=8d47811c6154d347, https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=535484d6482b80f4, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1 ecology/ENA_Biodiv_submission, microbiome/mgnify-amplicon
fastq_groomer fastq_groomer Convert between various FASTQ quality formats. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3066 3798 107854 130022 8079 45933 145592 914641 656 1191 15303 28714 206 208 7929 8019 1081396 276678 51130 12007 https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=70b1c40b818cc320, https://usegalaxy.eu/published/workflow?id=7117dbcbd5d12de5, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c7e1aee909c9b483, https://usegalaxy.eu/published/workflow?id=cf9dc7ad34c81fa2, https://usegalaxy.eu/published/workflow?id=eb3cfa4d1f05fc0e, https://usegalaxy.eu/published/workflow?id=f39528391f22aab0, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, https://usegalaxy.org.au/published/workflow?id=1ac197bae296b2bf, https://usegalaxy.org.au/published/workflow?id=39bb22274ede7500, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://usegalaxy.org.au/published/workflow?id=581c455f74aa55a4, https://usegalaxy.org.au/published/workflow?id=60c5675ed2f4a7d8, https://usegalaxy.org.au/published/workflow?id=e045a6064ad5fdc4, 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https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f2465afbdfc8ad46, https://usegalaxy.org/published/workflow?id=f39603063febba82, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://usegalaxy.org/published/workflow?id=f58970e6914a1bba, https://usegalaxy.org/published/workflow?id=f857e8282af234e0, https://usegalaxy.org/published/workflow?id=f895ed9fb68d3379, https://usegalaxy.org/published/workflow?id=fe2d15d352a9919f, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 ecology/ENA_Biodiv_submission, ecology/Obitools-metabarcoding, sequence-analysis/Manage_AB1_Sanger
fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 180 285 5124 6437 622 2173 5410 15997 86 164 3990 5357 15 15 503 503 28294 15027 2637 903 https://usegalaxy.eu/published/workflow?id=7734928ebc0a2654, https://usegalaxy.org.au/published/workflow?id=5926a7669eabb1c6, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://workflowhub.eu/workflows/1673?version=1 transcriptomics/srna
fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 58 61 675 733 244 1008 2111 8416 13 21 398 577 8 8 34 34 9760 3218 1098 323 https://usegalaxy.org/published/workflow?id=958f78270fc8f55c, https://usegalaxy.org/published/workflow?id=aef91b21e3b72f70 sequence-analysis/Manage_AB1_Sanger
fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 561 775 8915 13227 1973 2832 14532 22941 202 284 2045 3031 57 57 730 730 39929 26222 3948 2793 https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0
fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2968 3318 27989 31403 4447 5152 25343 30506 1649 1748 7253 8107 135 135 1103 1103 71119 61688 10353 9199 https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=95cb04ffb473623b, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e, https://usegalaxy.org.au/published/workflow?id=30430b75d05f54eb, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org.au/published/workflow?id=7fa13ccbf044edc5, https://usegalaxy.org.au/published/workflow?id=83e3ceceb1a92493, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=8b6739a000780d99, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=ee7a1615f187391d, https://usegalaxy.org.au/published/workflow?id=f25a05070bf97ded, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=0a57740c68e85e21, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=c446105e87750aa2, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/1444?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1622?version=1, https://workflowhub.eu/workflows/365?version=1 assembly/general-introduction, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 570 793 12982 18847 1661 5991 21263 61308 152 243 1664 2619 25 25 236 236 83010 36145 7052 2408 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=bab0322cc0346d81, https://usegalaxy.org/published/workflow?id=5df593510c7d944d, https://usegalaxy.org/published/workflow?id=6c7d320ad951f445, https://usegalaxy.org/published/workflow?id=8d3557a82f49528c, https://usegalaxy.org/published/workflow?id=c337e5265a8079d0, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22, https://usegalaxy.org/published/workflow?id=eeffba361f12a22d
fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 515 636 4433 4974 1317 3616 27563 40409 209 281 865 1229 17 17 45 45 46657 32906 4550 2058 https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac
fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 126 192 1189 1420 2021 9265 12840 61870 36 63 207 541 13 13 89 90 63921 14325 9533 2196 https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 48 58 279 380 216 2253 1115 9736 14 30 1232 1623 4 4 21 21 11760 2647 2345 282 https://usegalaxy.org/published/workflow?id=3767c9c07462b777
fastq_quality_filter cshl_fastq_quality_filter Filter by quality 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4665 5314 37994 40749 6202 14016 45014 145519 1994 2474 8377 11391 335 340 1344 1394 199053 92729 22144 13196 https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=13da0b6780007d12, https://usegalaxy.eu/published/workflow?id=1502fd3fa90d32d8, https://usegalaxy.eu/published/workflow?id=1d0f438faa441c4e, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=2aac571c44e6a7c8, https://usegalaxy.eu/published/workflow?id=38c7fa2653c5a2ee, https://usegalaxy.eu/published/workflow?id=39bf638cd7b56fd6, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=63749bd3045ccd4a, https://usegalaxy.eu/published/workflow?id=71cac07a151f9470, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=9a1d17c12b139bda, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=bd74a116e3f8d5b8, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=ccec1752fcac5e3f, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.eu/published/workflow?id=da3a6d229e422dde, https://usegalaxy.eu/published/workflow?id=db63d53712d2571b, https://usegalaxy.eu/published/workflow?id=dbcf7af09e036754, https://usegalaxy.eu/published/workflow?id=e47351e2edd93a1a, https://usegalaxy.eu/published/workflow?id=e6c5fb1d37d29ec0, https://usegalaxy.eu/published/workflow?id=e85c9385870aadcc, https://usegalaxy.eu/published/workflow?id=f0209559f3686fcc, https://usegalaxy.eu/published/workflow?id=f81534f6cf8733e7, https://usegalaxy.org.au/published/workflow?id=0ed947e76a69028b, https://usegalaxy.org.au/published/workflow?id=5a0fc3b91ae47788, https://usegalaxy.org.au/published/workflow?id=acaca80c4a0c76c8, https://usegalaxy.org.au/published/workflow?id=b46bc04e0418fdfa, https://usegalaxy.org.au/published/workflow?id=c622bd03677314aa, https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010, https://usegalaxy.org/published/workflow?id=0555313573cd1ee2, https://usegalaxy.org/published/workflow?id=0816aa5461c390d2, https://usegalaxy.org/published/workflow?id=08edef22fa132799, https://usegalaxy.org/published/workflow?id=0d6a4dfbccafd2a2, https://usegalaxy.org/published/workflow?id=0f43fdfe1824e9d7, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=26b2057a8bc0386c, https://usegalaxy.org/published/workflow?id=3e6d4ab34de7918c, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=58a7a02dade085cf, https://usegalaxy.org/published/workflow?id=58a91a914e381dcf, https://usegalaxy.org/published/workflow?id=58ceaed0a42fe60a, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6c49d9c25ba4ddf5, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=947340358dd268ea, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271, https://usegalaxy.org/published/workflow?id=cd3bce36b6ef073d, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://workflowhub.eu/workflows/1481?version=1 introduction/galaxy-intro-short
fastq_stats fastq_stats FASTQ Summary Statistics by column 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 678 941 3662 5208 2614 14639 13510 84786 161 293 3484 4398 53 53 296 296 94688 20952 15926 3506 https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.org/published/workflow?id=0017c434354b6f6a, https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3, https://usegalaxy.org/published/workflow?id=165c8a58baffe64c, https://usegalaxy.org/published/workflow?id=24adb067c82862fa, https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1, https://usegalaxy.org/published/workflow?id=4339d5625c15ae78, https://usegalaxy.org/published/workflow?id=6f436066dffbc37d, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c, https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=e35ac40c58953f74, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=f201ce61becf9a80, https://usegalaxy.org/published/workflow?id=f3983646b6df24bf
fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2014 2152 50989 55713 3019 7213 46867 109930 530 837 10769 18067 211 211 3227 3227 186937 111852 10413 5774 https://usegalaxy.eu/published/workflow?id=1b43449ed8481892, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://workflowhub.eu/workflows/1723?version=1 ecology/eDNA-taxonomic-analysis, sequence-analysis/Manage_AB1_Sanger
fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 314 388 13805 20661 637 1959 14158 34744 78 113 6297 7058 27 27 2036 2036 64499 36296 2487 1056 https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1e1a299825f27f11, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5de035c08af915ea, https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://workflowhub.eu/workflows/1629?version=1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 contributing/create-new-tutorial, sequence-analysis/Manage_AB1_Sanger, single-cell/scrna-data-ingest
fastq_trimmer fastq_trimmer FASTQ Trimmer by quality 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 603 788 10307 12822 1895 9246 22836 96214 118 245 2064 3428 16 16 156 156 112620 35363 10295 2632 https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.org.au/published/workflow?id=79572be1bf642251, https://usegalaxy.org.au/published/workflow?id=a3efc48b5992374e, https://usegalaxy.org.au/published/workflow?id=b518ee5540ed01fd, https://usegalaxy.org.au/published/workflow?id=d0933b5040adf902, https://usegalaxy.org.au/published/workflow?id=d1b604a5441dc4b0, https://usegalaxy.org/published/workflow?id=14410527253c6f40, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=462261c5e22635f0, https://usegalaxy.org/published/workflow?id=48dd684196c65735, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=ada910fc3a68757a, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3
fastqc fastqc Read QC reports using FastQC 2017-01-11 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 0.74+galaxy1 fastqc 0.12.1 To update Fastq Manipulation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis Sequencing, Data quality management, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. 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fastqe fastqe FASTQE 2020-07-13 https://fastqe.com/ 0.3.1+galaxy0 fastqe 0.3.3 To update Sequence Analysis Sequencing quality control Sequencing quality control Sequence analysis, Sequencing Sequence analysis, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3154 3177 6904 6978 6143 6198 13534 13627 1316 1323 3505 3549 291 291 510 510 24664 24453 10989 10904 https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=340aa3ae5468deb0, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=519e0ffdfd1790bc, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.org.au/published/workflow?id=115151c2c8998d44, https://usegalaxy.org.au/published/workflow?id=178db14511c8f293, https://usegalaxy.org.au/published/workflow?id=1f63ec596e578b1c, https://usegalaxy.org.au/published/workflow?id=2afeae1ec03c0b57, https://usegalaxy.org.au/published/workflow?id=43f2dabbc1932e30, https://usegalaxy.org.au/published/workflow?id=47cacc06d404a8c6, https://usegalaxy.org.au/published/workflow?id=5d6773ed5b2f41cb, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=bd251174d94cde9d, https://usegalaxy.org.au/published/workflow?id=dd6f465ab1eb10b0, https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a, https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=cf2dbc29ca20ebee, https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e sequence-analysis/quality-control
fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3845 4522 249408 274687 5714 14677 147702 280466 876 876 22007 22007 3 3 3 3 577163 419120 20078 10438 https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org.au/published/workflow?id=5cd804644a34c8fd, https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=400c1d170f073279, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=5c7f3d73543da895, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6c7d320ad951f445, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=93810012f2610de4, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22, https://usegalaxy.org/published/workflow?id=eeffba361f12a22d, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/794?version=2 ecology/ENA_Biodiv_submission, galaxy-interface/ncbi-sarf, microbiome/mgnify-amplicon
fastspar fastspar, fastspar_pvalues, fastspar_reduce Tool for rapid and scalable correlation estimation for compositional data. 2025-06-16 https://github.com/scwatts/fastspar/ 1.0.0 fastspar 1.0.0 Up-to-date Metagenomics, Statistics Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar FastSpar FastSpar FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1
fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL 2018-02-02 http://www.microbesonline.org/fasttree/ 2.1.10 fasttree 2.2.0 To update Phylogenetics Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1826 1923 84447 85175 2879 3069 29857 32881 829 967 8573 9437 82 84 411 416 127909 123288 6043 5616 https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=a484a1e1a7335696, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1559?version=1 evolution/abc_intro_phylo, evolution/bacterial-comparative-genomics, microbiome/pathogen-detection-from-nanopore-foodborne-data
fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 73 114 1004 2340 265 2463 3432 26090 27 55 666 1270 3 3 4 4 29704 5106 2635 368 https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=947340358dd268ea, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f
fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259 312 37602 40250 977 2966 52272 112642 57 80 868 1228 16 16 49 49 154169 90791 3374 1309 https://usegalaxy.org/published/workflow?id=87b6bac79f99c1f8, https://usegalaxy.org/published/workflow?id=cd431e5f912d3616
fastx_clipper cshl_fastx_clipper Clip adapter sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 236 294 3335 4086 1087 6193 14946 122932 41 65 478 882 6 6 27 27 127927 18786 6558 1370 https://usegalaxy.org/published/workflow?id=29a80db9f3208c29, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=77e4bb9d6aea0c9a, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=b0a12221ce09c001, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed
fastx_collapser cshl_fastx_collapser Collapse sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 401 459 59500 89761 876 3332 82238 206527 71 97 23810 25032 43 44 223 233 321553 165771 3932 1391 https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=1a6f552cfe798883, https://usegalaxy.org/published/workflow?id=23bca854e549ad48, https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1, https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a, https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6, https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9, https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29, https://usegalaxy.org/published/workflow?id=52e099f693639115, https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c, https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f, https://usegalaxy.org/published/workflow?id=74fe080f24f7da84, https://usegalaxy.org/published/workflow?id=80afe572b6693ca1, https://usegalaxy.org/published/workflow?id=98286b6154e1b57f, https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89, https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3, https://usegalaxy.org/published/workflow?id=de9c2db125a5ea27, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22
fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 55 98 140 293 1246 4541 5121 26678 73 105 1083 1309 8 9 11 12 28292 6355 4753 1382 https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274
fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 145 219 2175 2409 4427 11117 34705 77345 292 343 3332 3945 5 5 65 65 83764 40277 11684 4869 https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274
fastx_renamer cshl_fastx_renamer Rename sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 224 280 4631 5145 276 1075 9882 15505 54 75 498 834 13 13 632 632 22116 15643 1443 567 https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044, https://usegalaxy.org/published/workflow?id=1a6f552cfe798883, https://usegalaxy.org/published/workflow?id=23bca854e549ad48, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1, https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a, https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6, https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9, https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29, https://usegalaxy.org/published/workflow?id=52e099f693639115, https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c, https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f, https://usegalaxy.org/published/workflow?id=74fe080f24f7da84, https://usegalaxy.org/published/workflow?id=80afe572b6693ca1, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89, https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3
fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 456 552 11586 15931 593 1664 17732 70434 82 105 853 1100 22 22 3557 3557 91022 33728 2343 1153 https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=58a7a02dade085cf, https://usegalaxy.org/published/workflow?id=b18a41e364650fee, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 sequence-analysis/Manage_AB1_Sanger
fastx_trimmer cshl_fastx_trimmer Trim sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 658 834 14961 18093 1662 8605 113603 224353 223 293 3364 5948 257 258 1669 1672 250066 133597 9990 2800 https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=987a2abb5cd56e57, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.org/published/workflow?id=5641d1cbe795203f, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed, https://usegalaxy.org/published/workflow?id=e7030b62a3335bd7
featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome 2016-02-09 https://subread.sourceforge.net/ 2.1.1 subread 2.1.1 Up-to-date RNA, Transcriptomics, Sequence Analysis Read summarisation, RNA-Seq quantification Read summarisation, RNA-Seq quantification RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. 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feelnc feelnc Galaxy wrapper for FEELnc 2018-03-27 https://github.com/tderrien/FEELnc 0.2.1 feelnc 0.2 To update Sequence Analysis Annotation, Classification Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 139 151 1531 1740 143 156 1171 1283 8 8 115 115 15 15 71 71 3209 2888 330 305 https://workflowhub.eu/workflows/1324?version=1, https://workflowhub.eu/workflows/1484?version=1 genome-annotation/lncrna
fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. 2017-01-05 https://github.com/lh3/fermikit r193 fermi2 r193 Up-to-date Assembly, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fgsea fgsea Perform gene set testing using fgsea 2018-10-19 https://bioconductor.org/packages/release/bioc/html/fgsea.html 1.8.0+galaxy1 bioconductor-fgsea 1.32.2 To update Visualization, Transcriptomics, Statistics, Single Cell Gene-set enrichment analysis Gene-set enrichment analysis Genetics Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 632 734 7520 8942 1072 1156 22759 24664 121 136 1144 1277 9 9 115 115 34998 31538 2035 1834 https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=73a9ab4f0f0b9907, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://workflowhub.eu/workflows/1699?version=1 transcriptomics/rna-seq-genes-to-pathways
filtlong filtlong Filtlong - Filtering long reads by quality 2018-09-14 https://github.com/rrwick/Filtlong 0.3.1 filtlong 0.3.1 Up-to-date Fastq Manipulation, Sequence Analysis Filtering, Sequencing quality control Filtering, Sequencing quality control iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2169 2318 79820 82849 1410 1424 72145 72255 830 830 17538 17538 27 27 150 150 172792 169653 4599 4436 https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c3bfedf33bb00069, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org.au/published/workflow?id=fc664a96d8099652, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=cc6ee582a6e5cae2, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://workflowhub.eu/workflows/1613?version=1, https://workflowhub.eu/workflows/51?version=1 assembly/mrsa-nanopore
flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. 2020-11-06 https://github.com/BrooksLabUCSC/flair 1.5 flair 2.2.0 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 29 29 2028 2028 0 0 0 0 0 0 0 0 0 0 0 0 2028 2028 29 29 https://usegalaxy.eu/published/workflow?id=d4a6fb334f5dd10e
flash flash Fast Length Adjustment of SHort reads 2017-09-25 https://ccb.jhu.edu/software/FLASH/ 1.2.11 flash 1.2.11 Up-to-date Assembly, Fastq Manipulation Read pre-processing, Sequence merging, Sequence assembly Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 257 325 36629 39853 417 787 10871 18175 1 1 4 4 0 0 0 0 58032 47504 1113 675 https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=987a2abb5cd56e57, https://workflowhub.eu/workflows/100?version=1
fraggenescan fraggenescan Tool for finding (fragmented) genes in short read 2017-09-04 https://sourceforge.net/projects/fraggenescan/ fraggenescan 1.32 To update Sequence Analysis Gene prediction Gene prediction Genetics, Sequence analysis Genetics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 160 193 1267 1643 0 0 0 0 48 48 1171 1208 2 2 12 12 2863 2450 243 210 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=d57d41e306241396
freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool 2017-01-11 https://github.com/ekg/freebayes 1.3.10 freebayes 1.3.10 Up-to-date Variant Analysis Variant calling, Statistical calculation Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Genomics, Genetic variation, Rare diseases devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 8440 9638 175340 204865 14740 26159 140150 287235 1921 2607 23952 29522 246 246 2943 2946 524568 342385 38650 25347 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https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/676?version=1 proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, variant-analysis/dip, variant-analysis/dunovo, variant-analysis/exome-seq, variant-analysis/non-dip, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants
freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation 2022-07-05 https://github.com/andersen-lab/Freyja 2.0.1 freyja 2.0.1 Up-to-date Metagenomics, Sequence Analysis RNA-Seq quantification RNA-Seq quantification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 58 58 24576 24576 15 15 327 327 0 0 0 0 0 0 0 0 24903 24903 73 73 https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b
funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. 2021-08-26 https://funannotate.readthedocs.io 1.8.17 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 891 891 14118 14118 209 209 1453 1453 310 310 8597 8597 88 88 1505 1505 25673 25673 1498 1498 https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/754?version=1 ecology/phylogeny-data-prep, genome-annotation/funannotate
gamma gamma_s, gamma Gene Allele Mutation Microbial Assessment 2025-08-06 https://github.com/rastanton/GAMMA 2.2 GAMMA 2.2 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gatk4_mutect2 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK 2019-10-28 https://software.broadinstitute.org/gatk/gatk4 4.1.7.0 gatk4 4.6.2.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 564 611 3976 4606 1831 2022 10954 11924 0 0 0 0 0 0 0 0 16530 14930 2633 2395 https://usegalaxy.eu/published/workflow?id=93e32219d412c1f1, https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730, https://usegalaxy.org/published/workflow?id=2f21358621337cf2, https://usegalaxy.org/published/workflow?id=39753cc73284963f, https://usegalaxy.org/published/workflow?id=eb33df15225b8aa0, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=eed1aadf2fb83f6c, https://workflowhub.eu/workflows/35?version=1
gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format 2017-06-23 http://bioinf.iasi.cnr.it/gdcwebapp/ 1.0.0 python To update Data Source, Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gecko gecko Ungapped genome comparison 2020-11-25 https://github.com/otorreno/gecko 1.2 gecko 1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 341 341 1081 1081 0 0 0 0 124 124 961 961 0 0 0 0 2042 2042 465 465 https://workflowhub.eu/workflows/1541?version=1 genome-annotation/hpc-for-lsgc
gem_tools gem_check_memote, gem_escher_visualization, gem_extract_exchange, gem_flux_distribution, gem_flux_variability_analysis, gem_knockout, gem_phenotype_phase_plane Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries. 2024-12-01 https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology 0.29.1 cobra 0.21.0 To update Metabolomics, Systems Biology, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools 0 7 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 464 464 0 0 0 0 464 464 1 1
gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation 2014-11-09 https://github.com/arq5x/gemini 0.20.1 gemini 0.30.2 To update Sequence Analysis, Next Gen Mappers Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1258 1488 4490 6130 529 529 1823 1949 439 453 4187 4642 26 26 82 82 12803 10582 2496 2252 https://usegalaxy.eu/published/workflow?id=2aede5c6577b28f5, https://usegalaxy.eu/published/workflow?id=3570835f21365be7, https://usegalaxy.eu/published/workflow?id=b3b094f1bdbaa04a, https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://usegalaxy.eu/published/workflow?id=b82a4065be048ef6, https://usegalaxy.org.au/published/workflow?id=1be22b394f9ec3ab, https://usegalaxy.org.au/published/workflow?id=5442f0437ade82c4, https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c, https://workflowhub.eu/workflows/1636?version=1, https://workflowhub.eu/workflows/1655?version=1, https://workflowhub.eu/workflows/1668?version=1, https://workflowhub.eu/workflows/1672?version=1, https://workflowhub.eu/workflows/363?version=2 variant-analysis/dip, variant-analysis/exome-seq, variant-analysis/trio-analysis
gemini glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. 2017-11-28 https://ccb.jhu.edu/software/glimmer/ 3.02 glimmer 3.02 Up-to-date Sequence Analysis Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 390 390 6567 6567 0 0 0 0 0 0 0 0 0 0 0 0 6567 6567 390 390 https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep
genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals 2020-08-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1 1 1 1 0 1 0 0 0 1 0 0 0 1 1 1 0 1 0 0 0 1 1 0 0 0 0 1 0 1 1 1 1 2 2 4 4 16 280 152 2906 0 0 0 0 0 0 0 0 2910 156 282 18
genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility 2017-11-27 https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 3.0.0 ghm 3.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. 2023-06-20 https://github.com/iobio/gene.iobio 4.7.1+galaxy1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 172 172 0 0 0 0 8 8 158 158 0 0 0 0 330 330 56 56 https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://workflowhub.eu/workflows/1636?version=1 variant-analysis/trio-analysis
genetrack genetrack Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. 2015-12-18 numpy To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 203 228 674 0 0 0 0 0 0 0 0 674 228 203 78
genomescope genomescope Analyze unassembled short reads 2021-04-30 https://github.com/tbenavi1/genomescope2.0 2.0.1 genomescope2 2.1.0 To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1029 1029 5878 5878 641 641 3149 3149 261 261 2337 2337 37 37 614 614 11978 11978 1968 1968 https://usegalaxy.eu/published/workflow?id=0ccb3838765a8b84, https://usegalaxy.eu/published/workflow?id=0e642b5407dd595b, https://usegalaxy.eu/published/workflow?id=0fef06a87389eb59, https://usegalaxy.eu/published/workflow?id=10bde4e7f8dbd0c4, https://usegalaxy.eu/published/workflow?id=11ce7a7bf3d075e0, https://usegalaxy.eu/published/workflow?id=238606356787b876, https://usegalaxy.eu/published/workflow?id=29b4710cd24995b2, https://usegalaxy.eu/published/workflow?id=3069c17b52decab4, https://usegalaxy.eu/published/workflow?id=3788bb24b97f7b83, https://usegalaxy.eu/published/workflow?id=41c48e4632684f76, https://usegalaxy.eu/published/workflow?id=7f5da1ebd6673841, https://usegalaxy.eu/published/workflow?id=a85be448600a6789, https://usegalaxy.eu/published/workflow?id=acd29212884f967b, https://usegalaxy.eu/published/workflow?id=acfc7d1b03d5fbd0, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=c2c7f1815c411bfb, https://usegalaxy.eu/published/workflow?id=c4877de66200667b, https://usegalaxy.eu/published/workflow?id=d1e3d3bb0922d771, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=db6640887b5ca0cd, https://usegalaxy.eu/published/workflow?id=dec16871152fac35, https://usegalaxy.eu/published/workflow?id=ff16623a63ff5124, https://usegalaxy.org.au/published/workflow?id=049f61f436ff66df, https://usegalaxy.org.au/published/workflow?id=141ac7a106e49d8f, https://usegalaxy.org.au/published/workflow?id=26b57e0b79ea4559, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=5364e6ec5b4f48cd, https://usegalaxy.org.au/published/workflow?id=6aaaa084d5339c08, https://usegalaxy.org.au/published/workflow?id=6c54e7f7a4bf17ed, https://usegalaxy.org.au/published/workflow?id=6c5b84bcac127272, https://usegalaxy.org.au/published/workflow?id=8dc05e3ba64e981f, https://usegalaxy.org.au/published/workflow?id=ab9f7a97baaa7fa6, https://usegalaxy.org.au/published/workflow?id=b9d0a39d72b8e5f8, https://usegalaxy.org.au/published/workflow?id=c0aa1f64a89a6115, https://usegalaxy.org.au/published/workflow?id=d7c2d0d49b1a6c86, https://usegalaxy.org.au/published/workflow?id=d9ee934bbae0fa01, https://usegalaxy.org/published/workflow?id=14dc039ee7138b8b, https://usegalaxy.org/published/workflow?id=19e2191687f81c21, https://usegalaxy.org/published/workflow?id=2759eaa8adbd2857, https://usegalaxy.org/published/workflow?id=333c5725006e4154, https://usegalaxy.org/published/workflow?id=49e2570e363fda11, https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=7f8d7595cbeebf1d, https://usegalaxy.org/published/workflow?id=815cd221eaaaeb53, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://usegalaxy.org/published/workflow?id=9bc46b4d35749b41, https://usegalaxy.org/published/workflow?id=9f1aabc6f5d18d13, https://usegalaxy.org/published/workflow?id=a00f78b74c27b5f3, https://usegalaxy.org/published/workflow?id=ae71399852f34680, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://usegalaxy.org/published/workflow?id=bcf3ff03326c80b7, https://usegalaxy.org/published/workflow?id=beefb67de2b0728c, https://usegalaxy.org/published/workflow?id=c72f94a30ad54327, https://usegalaxy.org/published/workflow?id=faa4f94f070c6213, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1608?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/223?version=1, https://workflowhub.eu/workflows/365?version=1, https://workflowhub.eu/workflows/366?version=1, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/632?version=12, https://workflowhub.eu/workflows/698?version=1 assembly/ERGA-post-assembly-QC, assembly/largegenome, assembly/vgp_genome_assembly
genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases 2022-01-12 https://github.com/shbrief/GenomicSuperSignature 1.2.0 bioconductor-genomicsupersignature 1.14.0 To update Sequence Analysis, RNA, Transcriptomics Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 58 58 0 0 0 0 0 0 0 0 0 0 0 0 58 58 20 20
genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). 2019-07-05 https://github.com/jsh58/Genrich 0.5+galaxy2 genrich 0.6.1 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 283 435 2214 3829 460 460 3086 3086 31 31 700 703 0 0 0 0 7618 6000 926 774 https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb
geopandas geopandas_table2geojson GeoPandas is an open source project to make working with geospatial data easier. 2025-04-20 https://geopandas.org 1.1.1 geopandas To update Geo Science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 41 41 0 0 0 0 0 0 0 0 0 0 0 0 41 41 3 3
get_hrun get_hrun Annotate indel variants with homopolymer context 2021-03-02 https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun 0.5.9.2 pyfaidx 0.9.0.3 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 9 9 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5
getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. 2022-03-15 https://github.com/Kinggerm/GetOrganelle 1.7.7.1 getorganelle 1.7.7.1 Up-to-date Assembly De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 403 403 9423 9423 0 0 0 0 108 108 1588 1588 0 0 0 0 11011 11011 511 511 https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59
gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format 2019-06-18 http://gfa-spec.github.io/GFA-spec/ 0.1.2 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 911 1010 9926 11805 621 661 6768 7202 186 188 1778 1807 52 52 228 228 21042 18700 1911 1770 https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=fba1671d835b6dd3, https://usegalaxy.org.au/published/workflow?id=044b6b475b4db27a, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=36604d0ab0dee988, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=98d3def7da131b4c, https://usegalaxy.org.au/published/workflow?id=afab89bc468da8b3, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=f83a3cda33131fb8, https://workflowhub.eu/workflows/1162?version=2, https://workflowhub.eu/workflows/1163?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/221?version=3, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/605?version=1, https://workflowhub.eu/workflows/606?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/789?version=1 assembly/hifi-assembly, assembly/vgp_genome_assembly, microbiome/plasmid-metagenomics-nanopore
gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 80 83 1290 1337 42 45 179 207 12 12 182 182 1 1 1 1 1727 1652 141 135 https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6
gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. 2017-03-27 https://github.com/gpertea/gffcompare/ 0.12.10 gffcompare 0.12.10 Up-to-date Transcriptomics Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1157 1332 4195 5221 1776 2918 5168 9180 179 272 1521 2011 29 29 79 79 16491 10963 4551 3141 https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=2287afbf248d9c89, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=e8202b7b6338005d, https://usegalaxy.eu/published/workflow?id=f026c4b8341ff94c, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=53010c2f1f207429, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org.au/published/workflow?id=e045a6064ad5fdc4, https://usegalaxy.org/published/workflow?id=31c35b9a93237235, https://usegalaxy.org/published/workflow?id=4061e061f659449b, https://usegalaxy.org/published/workflow?id=454d7310d001a4d0, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=8700f593a3d642f5, https://usegalaxy.org/published/workflow?id=9c022f4028de0bc6, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1685?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1788?version=1 proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/differential-isoform-expression
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ggplot2_heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package 2019-02-10 https://github.com/cran/gplots 3.2.0 r-gplots 2.17.0 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5453 6454 52101 62236 6555 8257 69586 84002 840 946 8530 9871 281 285 2996 3046 159155 133213 15942 13129 https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=511b023121b7c488, https://usegalaxy.eu/published/workflow?id=63964ba7d9edce74, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=68e8042f11d5a3fd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=81f1927bfe3ffea1, https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a65a17122d2234a8, https://usegalaxy.eu/published/workflow?id=a7dc6e0c43cb6d6d, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.eu/published/workflow?id=d6f7e86d52d43555, https://usegalaxy.eu/published/workflow?id=dfee2bd4e4600ad9, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=f58526da1fd68108, https://usegalaxy.eu/published/workflow?id=f78e16c669481efd, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org.au/published/workflow?id=04ab43fb3e7840ef, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=28705b86e0595ded, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://usegalaxy.org.au/published/workflow?id=42305ed876d19d08, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=7ef245f5ae3b916d, https://usegalaxy.org.au/published/workflow?id=84a8eb379440656e, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=8eab5e2b2c683076, https://usegalaxy.org.au/published/workflow?id=8fb691706f47527a, https://usegalaxy.org.au/published/workflow?id=a9e59d38c6c710bc, https://usegalaxy.org.au/published/workflow?id=ae773dfaa074cb72, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org.au/published/workflow?id=e4ddf33ee5b5e259, https://usegalaxy.org.au/published/workflow?id=f7fd24318c4bf949, https://usegalaxy.org/published/workflow?id=19fcce20ecaf2ef6, https://usegalaxy.org/published/workflow?id=25cdc47baba556c5, https://usegalaxy.org/published/workflow?id=40a65b5bc1dcc0b4, https://usegalaxy.org/published/workflow?id=4c840284d2984fa0, https://usegalaxy.org/published/workflow?id=667493d318b86b7d, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=abf1aec0f3d48d03, https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1426?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1718?version=1 proteomics/maxquant-msstats-dda-lfq, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-viz-with-heatmap2
ggupset emc-ggupset Create Upset Plots with ggupset 2022-12-17 https://github.com/const-ae/ggupset 1.0 r-ggupset To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. 2018-12-28 https://github.com/DanFaria/GOEnrichment 2.0.1 goenrichment 2.0.1 Up-to-date Genome annotation Gene-set enrichment analysis Gene-set enrichment analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 799 928 6000 7557 1081 1196 8060 9309 230 233 1602 1647 5 6 39 44 18557 15701 2363 2115 https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1667?version=1 single-cell/GO-enrichment, transcriptomics/goenrichment
goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html 1.50.0 bioconductor-goseq 1.58.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3196 3921 23708 28273 3528 4089 26762 31254 640 680 4461 5015 103 104 751 784 65326 55682 8794 7467 https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=c1a6d11e1eab6a42, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=4f0814ec9f9f8425, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=742120336d5ff997, https://workflowhub.eu/workflows/1194?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/689?version=1 transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways
gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more 2019-10-30 https://biit.cs.ut.ee/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 To update Statistics, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 550 584 4378 4901 792 850 8647 9196 0 0 0 0 0 0 0 0 14097 13025 1434 1342 https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1515?version=1 single-cell/GO-enrichment
graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information 2019-12-10 https://github.com/fabriziocosta/GraphEmbed 2.4 graph_embed 2.4 Up-to-date Statistics, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5 7 18 79 44 49 71 134 0 0 0 0 0 0 0 0 213 89 56 49
graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan graphlan 1.1.3 To update Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 799 940 11872 13928 325 325 1773 1773 202 207 1432 1470 21 21 90 90 17261 15167 1493 1347 https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot 1.1.2 groot 1.1.2 Up-to-date Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 7 7 0 0 0 0 0 0 0 0 3 3 37 37 44 44 8 8
gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format 2024-08-25 https://github.com/nick-youngblut/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Up-to-date Metagenomics Data handling, Mapping, Generation Data handling, Mapping, Generation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 1127 1127 0 0 0 0 0 0 0 0 0 0 0 0 1127 1127 27 27 https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1
gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.5.2 gtdbtk 2.5.2 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 462 462 3982 3982 305 305 1566 1566 177 177 1095 1095 15 15 1439 1439 8082 8082 959 959 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://workflowhub.eu/workflows/1352?version=3
gtftobed12 gtftobed12 Convert GTF files to BED12 format 2018-05-17 http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README 357 ucsc-gtftogenepred 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3876 4805 9565 11802 3850 4091 9783 10498 436 457 2010 2130 213 214 432 460 24890 21790 9567 8375 https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=2049d38325423cfe, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=8c4fcd4bd9d5a72d, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/878?version=1 transcriptomics/differential-isoform-expression, transcriptomics/ref-based
gubbins gubbins Gubbins - bacterial recombination detection 2017-06-22 3.2.1 gubbins 3.4.3 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 402 428 4731 5118 268 288 3847 4061 250 317 1977 2858 0 0 0 0 12037 10555 1033 920
gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. 2016-12-29 https://github.com/sequencing/gvcftools 0.1 gvcftools 0.17.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gwastools gwastools_manhattan_plot 2019-10-07 https://bioconductor.org/packages/release/bioc/html/GWASTools.html 0.1.0 bioconductor-gwastools 1.52.0 To update Visualization, Variant Analysis Deposition, Analysis, Annotation Deposition, Analysis, Annotation GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 26 26 26 26 6 6 https://usegalaxy.fr/published/workflow?id=1ad87b99f0cb828c
halfdeep halfdeep HalfDeep: Automated detection of intervals covered at half depth by sequenced reads. 2024-11-27 https://github.com/makovalab-psu/HalfDeep 0.1.0 halfdeep 0.1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 52 52 0 0 0 0 0 0 0 0 52 52 5 5
hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.1.9 To update Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 254 254 18459 18459 1 1 20 20 1 1 21 21 6 6 191 191 18691 18691 262 262 https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1
hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies 2022-10-19 https://github.com/vibansal/HapCUT2 1.3.4 hapcut2 1.3.4 Up-to-date Assembly Haplotype mapping, Variant classification Haplotype mapping, Variant classification galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 hapcut2 HapCUT2 HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 131 131 0 0 0 0 131 131 6 6
hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes 2022-09-16 https://github.com/institut-de-genomique/HAPO-G 1.3.8 hapog 1.3.8 Up-to-date Assembly Genome assembly, Optimisation and refinement Genome assembly, Optimisation and refinement Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 94 94 677 677 0 0 0 0 0 0 0 0 36 36 392 392 1069 1069 130 130
happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. 2022-01-25 https://github.com/Illumina/hap.py 0.3.14 hap.py 0.3.15 To update Variant Analysis Variant calling, Sequence analysis, Genotyping Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism Genomics, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. 2018-06-11 https://github.com/ls-cwi/heinz 1.0 bioconductor-bionet 1.66.0 To update Transcriptomics, Visualization, Statistics, Single Cell Pathway or network analysis Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks Genetics, Gene expression, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz heinz Heinz Tool for single-species active module discovery. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 123 160 823 1460 318 345 1490 1678 36 36 847 913 0 0 0 0 4051 3160 541 477 https://usegalaxy.eu/published/workflow?id=12c80c5b5e2305d8, https://usegalaxy.org.au/published/workflow?id=6a161c87d19a543c, https://workflowhub.eu/workflows/1677?version=1 transcriptomics/network-analysis-with-heinz
hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard 2024-06-07 https://github.com/VariantEffect/hgvsParseR/tree/master 0.1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 6353 6353 0 0 0 0 0 0 0 0 0 0 0 0 6353 6353 2 2
hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hicbuildmatrixmicroc, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 2017-08-24 https://github.com/deeptools/HiCExplorer 3.7.6 hicexplorer 3.7.6 Up-to-date Sequence Analysis, Visualization bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 38 38 39 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 35 33 0 354 633 40441 75024 55 55 2146 2146 27 27 5559 5584 1 1 2 2 82756 48148 716 437 https://usegalaxy.eu/published/workflow?id=2f053b615d9788bf, https://usegalaxy.eu/published/workflow?id=5cb54278075696ca, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1610?version=1, https://workflowhub.eu/workflows/1847?version=1 epigenetics/hicexplorer
hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices 2022-11-25 https://github.com/koszullab/hicstuff 3.2.4 hicstuff 3.2.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hifiasm hifiasm A fast haplotype-resolved de novo assembler 2024-07-11 https://github.com/chhylp123/hifiasm 0.25.0 hifiasm 0.25.0 Up-to-date Assembly bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 803 803 2713 2713 585 585 2136 2136 187 187 3817 3817 51 51 183 183 8849 8849 1626 1626 https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=01fe4c590e608103, https://usegalaxy.eu/published/workflow?id=023a0ee62dd1f593, https://usegalaxy.eu/published/workflow?id=03be9d62e8e4a129, https://usegalaxy.eu/published/workflow?id=085c3a4c89d137b5, https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511, https://usegalaxy.eu/published/workflow?id=1151052f4393852a, https://usegalaxy.eu/published/workflow?id=1483534f49b826bf, https://usegalaxy.eu/published/workflow?id=17b0a6d3379a4392, 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hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 2023-01-18 https://github.com/xfengnefx/hifiasm-meta 0.3.1 hifiasm_meta hamtv0.3.1 To update Metagenomics Sequence assembly Sequence assembly Sequence assembly, Metagenomics Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 229 229 0 0 0 0 16 16 368 368 0 0 0 0 597 597 56 56
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transcriptomics/minerva-pathways, transcriptomics/rna-seq-reads-to-counts, transcriptomics/srna
hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 2018-06-06 https://pypi.org/project/hivclustering/ 1.3.1 python-hivclustering 1.8.0 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 380 403 36302 43262 0 0 0 0 83 84 4731 4887 97 97 540 543 48692 41573 584 560 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1
htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) 2016-09-15 https://readthedocs.org/projects/htseq/ 2.0.9 htseq 2.0.9 Up-to-date Genomic Interval Operations, SAM, Sequence Analysis, RNA Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis lparsons https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3989 5200 135497 191189 11193 18984 254054 434409 2158 3031 21954 36591 552 555 16740 16789 678978 428245 27770 17892 https://usegalaxy.eu/published/workflow?id=006ea49456a2a8ca, https://usegalaxy.eu/published/workflow?id=0821ec1cb4d6f30b, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=0fa523529c4f73cf, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=5b46c8533cd95447, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=70b1c40b818cc320, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=9e03cf8cd5e5de08, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.eu/published/workflow?id=c7e1aee909c9b483, https://usegalaxy.eu/published/workflow?id=cf9dc7ad34c81fa2, https://usegalaxy.eu/published/workflow?id=d086340422009ba9, https://usegalaxy.eu/published/workflow?id=e5f6d12e08d7a13b, https://usegalaxy.eu/published/workflow?id=eb3cfa4d1f05fc0e, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.fr/published/workflow?id=e266db902aa1b0e8, https://usegalaxy.fr/published/workflow?id=ff14dc4005e92cfd, https://usegalaxy.org.au/published/workflow?id=16a2c2e8b3c1ffe6, https://usegalaxy.org.au/published/workflow?id=1a107e6611fb9c15, https://usegalaxy.org.au/published/workflow?id=a35e5a238a70176a, https://usegalaxy.org.au/published/workflow?id=b2818098da6e2f82, https://usegalaxy.org/published/workflow?id=0292971d1a87abba, https://usegalaxy.org/published/workflow?id=204d0da8a023d7da, https://usegalaxy.org/published/workflow?id=385ac7ec85e37e3e, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=413d7e5aa7378cf1, https://usegalaxy.org/published/workflow?id=41c09a87c6cd5f75, https://usegalaxy.org/published/workflow?id=4c0785fe74ab0a24, https://usegalaxy.org/published/workflow?id=62316da77b1bfa5a, https://usegalaxy.org/published/workflow?id=8fb8c80c93ad694e, https://usegalaxy.org/published/workflow?id=a86b1f1682bb4a62, https://usegalaxy.org/published/workflow?id=aafa51fdc172f4c5, https://usegalaxy.org/published/workflow?id=b0e19e7315b64c87, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=ce232859a466c75c, https://usegalaxy.org/published/workflow?id=d2f7fd589a91124a, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd, https://usegalaxy.org/published/workflow?id=dcf6f201b787d148, https://usegalaxy.org/published/workflow?id=e04f443a8ceca0d2, https://usegalaxy.org/published/workflow?id=e40c2e7f6b73fb11, https://usegalaxy.org/published/workflow?id=efb10012b8448b21, https://workflowhub.eu/workflows/412?version=1
humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 10 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 795 795 52483 52483 123 123 3171 3171 122 122 4812 4812 17 17 987 987 61453 61453 1057 1057 https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=fd733565098d76c9, https://workflowhub.eu/workflows/1447?version=2, https://workflowhub.eu/workflows/1456?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short
hybpiper hybpiper Analyse targeted sequence capture data 2023-08-30 https://github.com/mossmatters/HybPiper 2.1.6 hybpiper 2.3.3 To update Sequence Analysis, Phylogenetics Sequence trimming, Sequence assembly, Read mapping Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 1679 1679 0 0 0 0 6 6 258 258 0 0 0 0 1937 1937 15 15
hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.83 hyphy 2.5.84 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. 16 2 16 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 16 12 0 88 94 10953 11906 78 108 4725 8358 33 42 815 909 3 5 22 27 21200 16515 249 202 https://usegalaxy.eu/published/workflow?id=1d40d6deb2da04cc, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies 2021-11-15 https://github.com/kensung-lab/hypo 1.0.3 hypo 1.0.3 Up-to-date Assembly Optimisation and refinement, Genome assembly Optimisation and refinement, Genome assembly Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 107 107 575 575 0 0 0 0 0 0 0 0 0 0 0 0 575 575 107 107 https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1
icescreen icescreen identification of ICEs and IMEs in Bacillota genomes. 2022-01-04 https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.3 icescreen 1.3.3 Up-to-date Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 153 153 4 4 15 15 0 0 0 0 0 0 0 0 168 168 7 7
idba idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html idba 1.1.3 To update Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 106 126 944 1353 146 169 1199 1700 0 0 0 0 1 1 3 3 3056 2146 296 253
idr idr Galaxy wrappers for the IDR package from Nathan Boleu 2017-08-21 https://github.com/nboley/idr 2.0.3 idr 2.0.4.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 124 147 2665 3214 209 231 1828 2058 0 0 0 0 0 0 0 0 5272 4493 378 333 https://usegalaxy.eu/published/workflow?id=3817cfbab7b39ee1, https://usegalaxy.org/published/workflow?id=59d34b4f0178120b epigenetics/cut_and_run
idr_download_by_ids idr_download_by_ids Image Data Resource downloading tool 2020-02-04 https://idr.openmicroscopy.org 0.45 omero-py 5.11.1 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 46 232 457 0 0 0 0 1 1 445 445 0 0 0 0 902 677 47 38 https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://workflowhub.eu/workflows/1505?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/41?version=2 imaging/2D-spot-detection, imaging/tutorial-CP
iedb_api iedb_api Get epitope binding predictions from IEDB-API 2020-02-26 http://tools.immuneepitope.org/main/tools-api/ 2.15.2 python To update Data Source, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 38 43 3543 4425 6 6 33 33 3 3 234 234 0 0 0 0 4692 3810 52 47 https://usegalaxy.eu/published/workflow?id=9b4e6c5f2c1babce, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=832a30759469d3fe, https://usegalaxy.org/published/workflow?id=d0847ce8261eb922, https://workflowhub.eu/workflows/1406?version=1, https://workflowhub.eu/workflows/1789?version=1 proteomics/neoantigen-hla-binding-novel-peptides
infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data 2024-07-23 https://github.com/broadinstitute/infercnv 1.22.0 bioconductor-infercnv 1.22.0 Up-to-date Transcriptomics, Variant Analysis, Single Cell Heat map generation, Expression analysis, RNA-Seq analysis, Copy number variation detection, Clustering Heat map generation, RNA-Seq analysis, Copy number variation detection, Clustering iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv infercnv InferCNV Inferring copy number alterations from tumor single cell RNA-Seq data 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 31 31 0 0 0 0 0 0 0 0 0 0 0 0 31 31 7 7
instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes 2021-08-11 https://instrain.readthedocs.io/ 1.5.3 instrain 1.10.0 To update Metagenomics SNP detection, Genome comparison SNP detection, Genome comparison Mapping, Metagenomics Mapping, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 22 22 208 208 0 0 0 0 0 0 0 0 0 0 0 0 208 208 22 22
integronfinder integron_finder "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" 2022-09-22 https://github.com/gem-pasteur/Integron_Finder 2.0.5 integron_finder 2.0.6 To update Sequence Analysis Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 390 390 64428 64428 252 252 7167 7167 132 132 12061 12061 34 34 2504 2504 86160 86160 808 808 https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/bacterial-genome-annotation
intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter 2018-07-01 https://github.com/intermine 0.0.1 coreutils 8.25 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 14 15 53 10 17 21 90 1 1 159 159 0 0 0 0 302 195 32 18 https://workflowhub.eu/workflows/1398?version=1 galaxy-interface/intermine
interproscan interproscan Interproscan queries the interpro database and provides annotations. 2021-11-15 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ 5.59-91.0 interproscan 5.59_91.0 To update Sequence Analysis Sequence motif recognition, Protein feature detection Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Gene and protein families, Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2350 2550 44154 69658 486 486 3914 3914 799 804 13188 13204 144 144 9435 9435 96211 70691 3984 3779 https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a95556ec171d405, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 ecology/marine_omics_bgc, genome-annotation/funannotate, genome-annotation/functional
interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals 2020-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1+galaxy1 bx-python 0.14.0 To update Genomic Interval Operations Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. 1 1 1 1 0 0 0 0 0 1 0 0 0 1 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 1 1 0 6 10 21 107 82 1259 711 19652 2 2 23 31 1 1 7 7 19797 762 1272 91 https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=d3a69b0b826331ef
intervene intervene_pairwise, intervene_upset Create pairwise and upset plots 2018-09-11 https://intervene.readthedocs.io 0.6.5 intervene 0.6.5 Up-to-date Statistics Sequence comparison, Sequence visualisation Sequence comparison, Sequence visualisation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 270 284 1959 2152 274 295 4435 4873 0 0 0 0 0 0 0 0 7025 6394 579 544
ipfp_normalisation ipfp_norm Normalisation algorithm used to adjust matrices iteratively to satisfy specific row and column sum constraints while preserving the data structure. 2025-01-28 https://isoquac.net/ 0.1.0+galaxy0 numpy To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ipfp_normalisation https://github.com/galaxyproject/tools-iuc/tree/main/tools/ipfp_normalisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
iqtree iqtree Efficient phylogenomic software by maximum likelihood 2017-09-26 http://www.iqtree.org/ 2.4.0 iqtree 3.0.1 To update Phylogenetics Phylogenetic analysis, Sequence analysis Phylogenetic analysis, Sequence analysis Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2588 2695 44137 45132 2814 3035 34112 35898 1165 1337 16490 18756 17 17 229 229 100015 94968 7084 6584 https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=d5cf994c03a60fa4, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=952b83e52f7d7cff, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1839?version=1, https://workflowhub.eu/workflows/359?version=1 evolution/abc_intro_phylo, sequence-analysis/tapscan-streptophyte-algae, variant-analysis/aiv-analysis
irissv irissv Refine insertion sequences 2021-01-17 https://github.com/mkirsche/Iris 1.0.5 samtools 1.22.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 8 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 8 8
irma irma Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. 2024-11-09 https://wonder.cdc.gov/amd/flu/irma/irma.html 1.2.0 irma 1.2.0 Up-to-date Sequence Analysis Mapping assembly Mapping assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma irma-virus IRMA Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 16450 16450 0 0 0 0 0 0 0 0 0 0 0 0 16450 16450 12 12
isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. 2022-12-17 https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html 1.20.0 bioconductor-isoformswitchanalyzer 2.6.0 To update Transcriptomics, RNA, Statistics Sequence comparison, Sequence analysis Sequence comparison, Sequence analysis Computational biology, Gene transcripts Computational biology, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 107 107 2460 2460 126 126 2434 2434 21 21 1287 1287 2 2 12 12 6193 6193 256 256 https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 transcriptomics/differential-isoform-expression
ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing 2020-03-21 https://github.com/andersen-lab/ivar 1.4.4 ivar 1.4.4 Up-to-date Sequence Analysis Primer removal Primer removal Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar andersen-lab_ivar iVar iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1081 1087 1414011 1417441 1310 1330 147224 148408 374 379 43473 54915 19 19 7502 7502 1628266 1612210 2815 2784 https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, 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iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data 2017-06-08 https://bioconductor.org/packages/release/bioc/html/IWTomics.html 1.0.0 bioconductor-iwtomics 1.30.0 To update Statistics Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics iwtomics IWTomics Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 9 13 644 760 14 34 32 252 5 5 478 518 0 0 0 0 1530 1154 52 28 https://workflowhub.eu/workflows/1719?version=1 statistics/iwtomics
jasminesv jasminesv Merge structural variants across samples 2021-01-17 https://github.com/mkirsche/Jasmine/ 1.0.11 jasminesv 1.1.5 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15 15 94 94 25 25 62 62 0 0 0 0 0 0 0 0 156 156 40 40
jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool 2015-05-01 https://jbrowse.org 1.16.11 jbrowse 1.16.11 Up-to-date Sequence Analysis Genome visualisation Genome visualisation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. 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jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool 2021-09-30 https://jbrowse.org 3.6.5 jbrowse2 3.6.5 Up-to-date Sequence Analysis Genome visualisation, Structure visualisation, Pathway visualisation Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Mapping, Structural variation, Genomics, Gene structure, Sequence assembly fubar https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 626 626 3765 3765 349 349 1248 1248 95 95 603 603 0 0 0 0 5616 5616 1070 1070 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=84414f3441946702, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=ce8bf03d3df24806, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050 epigenetics/formation_of_super-structures_on_xi
jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) 2018-07-31 https://github.com/tanghaibao/jcvi 0.8.4 jcvi 1.5.7 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 761 859 3063 3622 833 902 2694 2899 611 616 1558 1578 49 49 439 439 8538 7754 2426 2254 https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=49b253f75ab6f38f, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1, https://workflowhub.eu/workflows/881?version=5 genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/helixer
jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA 2021-04-07 https://github.com/gmarcais/Jellyfish kmer-jellyfish 2.3.1 To update Assembly k-mer counting k-mer counting Sequence analysis, Genomics Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 369 369 4901 4901 0 0 0 0 87 87 1492 1492 35 35 1519 1519 7912 7912 491 491 https://usegalaxy.eu/published/workflow?id=bc32937d505135ab
join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier 2017-05-31 https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
jq jq JQ is a lightweight and flexible command-line JSON processor 2017-06-22 https://stedolan.github.io/jq/ 1.0 jq 1.5 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 72 510 2396 87 95 659 722 14 14 388 388 3 3 8 8 3514 1565 184 169 https://workflowhub.eu/workflows/245?version=1, https://workflowhub.eu/workflows/373?version=2, https://workflowhub.eu/workflows/374?version=1, https://workflowhub.eu/workflows/375?version=1 galaxy-interface/ncbi-sarf
jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics 2021-02-11 https://lindenb.github.io/jvarkit/ 20201223 jvarkit-wgscoverageplotter 20201223 Up-to-date SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 748 748 10984 10984 1487 1487 15150 15150 0 0 0 0 0 0 0 0 26134 26134 2235 2235 https://usegalaxy.eu/published/workflow?id=cd3398e29f375d97, https://usegalaxy.org/published/workflow?id=3dbe754882a263cd variant-analysis/tb-variant-analysis
kaiju kaiju_addtaxonnames, kaiju_mergeoutputs, kaiju_kaiju, kaiju_kaiju2krona, kaiju_kaiju2table taxonomic classification of high-throughput sequencing reads 2025-04-22 https://github.com/bioinformatics-centre/kaiju 1.10.1 kaiju 1.10.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju kaiju Kaiju Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2
kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. 2017-08-04 https://pachterlab.github.io/kallisto/ 0.48.0 kallisto 0.51.1 To update Transcriptomics Gene expression profiling Gene expression profiling Transcriptomics, RNA-Seq, Gene expression Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 892 996 31647 35827 2181 2848 76773 93407 210 242 6155 7133 17 17 564 564 136931 115139 4103 3300 https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3, https://usegalaxy.org/published/workflow?id=526b05cbffecbc85, https://usegalaxy.org/published/workflow?id=7d9bf3437e0a3d27, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0
kc_align kc-align Kc-Align custom tool 2020-02-20 https://github.com/davebx/kc-align 1.0.2 kcalign 1.0.2 Up-to-date Sequence Analysis Multiple sequence alignment Multiple sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments. Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment.Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 51 57 243 385 263 295 7653 8360 0 0 0 0 0 0 0 0 8745 7896 352 314 https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 98 116 1572 2262 169 185 1179 1564 25 25 2179 2179 0 0 0 0 6005 4930 326 292
king king Kinship-based INference for Gwas 2021-11-16 http://people.virginia.edu/~wc9c/KING/ 2.2.7 king 2.2.7 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/king https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 16 16 0 0 0 0 0 0 0 0 0 0 0 0 16 16 8 8
kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate 2.3.2 kleborate 3.2.4 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 123 123 1479 1479 0 0 0 0 0 0 0 0 0 0 0 0 1479 1479 123 123
kma kma_map Map with KMA 2019-10-30 https://bitbucket.org/genomicepidemiology/kma 1.5.1 kma 1.6.6 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 2 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 https://workflowhub.eu/workflows/407?version=1
kmer2stats kmer2stats A tool for creating data files for statistics based on kmers 2025-04-16 https://github.com/SantaMcCloud/kmer2stats 1.0.1 kmer2stats 1.0.1 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 310 310 0 0 0 0 0 0 0 0 0 0 0 0 310 310 8 8
kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan 1.3.0 kofamscan 1.3.0 Up-to-date Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 94 94 2904 2904 0 0 0 0 0 0 0 0 2 2 3 3 2907 2907 96 96 https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=d57d41e306241396
kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. 2017-01-24 http://ccb.jhu.edu/software/kraken/ kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. 5 5 5 5 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 1452 1453 75318 75385 2535 4229 59050 144905 904 1133 38078 44609 114 114 3720 3720 268619 176166 6929 5005 https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be
kraken2 kraken2 Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.1.3 kraken2 2.14 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics, Microbial ecology, Microbiology Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. 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kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) 2022-09-03 https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 Up-to-date Metagenomics Genome annotation, Taxonomic classification Genome annotation, Taxonomic classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom kraken-biom kraken-biom Create BIOM-format tables from Kraken output 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 857 857 4747 4747 47 47 150 150 95 95 963 963 9 9 17 17 5877 5877 1008 1008 https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea, https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://workflowhub.eu/workflows/1470?version=1 microbiome/taxonomic-profiling
kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report 2016-06-01 https://github.com/blankenberg/Kraken-Taxonomy-Report 0.0.3 biopython 1.70 To update Metagenomics Visualisation, Classification Visualisation, Classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1148 1155 5719 5735 1291 1717 5613 7684 148 148 587 587 10 10 25 25 14031 11944 3030 2597 https://usegalaxy.eu/published/workflow?id=2e5e6291cd112225, https://usegalaxy.eu/published/workflow?id=b659069edd9b1d4e
krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken 2023-01-13 https://github.com/jenniferlu717/KrakenTools 1.2.1 krakentools 1.2.1 Up-to-date Metagenomics Visualisation, Aggregation Visualisation, Aggregation Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files 6 6 6 6 0 0 0 0 0 0 0 0 0 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 1 0 2603 2603 161915 161915 1861 1861 40010 40010 488 488 18602 18602 64 64 5824 5824 226351 226351 5016 5016 https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=10101558b211a782, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99, https://usegalaxy.eu/published/workflow?id=f97e6fe1fcbc53a7, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=131636a795bac485, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://usegalaxy.org/published/workflow?id=3011f5dbf884c9bc, https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1059?version=1, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1431?version=1, https://workflowhub.eu/workflows/1439?version=1, https://workflowhub.eu/workflows/1470?version=1, https://workflowhub.eu/workflows/1483?version=1, https://workflowhub.eu/workflows/1492?version=2 microbiome/beer-data-analysis, microbiome/diversity, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling
krocus krocus Predict MLST directly from uncorrected long reads 2019-09-03 https://github.com/quadram-institute-bioscience/krocus 1.0.1 krocus 1.0.3 To update Sequence Analysis Multilocus sequence typing, k-mer counting Multilocus sequence typing, k-mer counting Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus krocus krocus Predict MLST directly from uncorrected long reads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. 2020-06-17 http://last.cbrc.jp/ 1205 last 1648 To update Sequence Analysis Sequence alignment Sequence alignment Genomics, Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last last LAST Short read alignment program incorporating quality scores 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 40 43 316 384 0 0 0 0 0 0 0 0 3 3 22 22 406 338 46 43
lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d 2018-02-12 https://github.com/lastz/lastz 1.04.22 lastz 1.04.52 To update Next Gen Mappers Sequence alignment, Read mapping Sequence alignment, Read mapping Genomics Genomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 493 570 57942 85720 758 3548 154432 208919 149 206 14671 39255 13 14 4663 4664 338558 231708 4338 1413 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://workflowhub.eu/workflows/1638?version=1 assembly/ecoli_comparison
lcrgenie lcrgenie Ligase Chain Reaction Genie 2022-12-02 https://github.com/neilswainston/LCRGenie 1.0.2 lcr_genie To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
legsta legsta Performs in silico Legionella pneumophila sequence based typing. 2022-02-21 https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 13 13 134 134 0 0 0 0 0 0 0 0 0 0 0 0 134 134 13 13
length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file 2016-11-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 To update Fasta Manipulation, Statistics, RNA, Micro-array Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 973 1056 4962 5219 1265 1410 2651 3077 123 123 317 317 8 8 14 14 8627 7944 2597 2369 https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1715?version=1 transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz
lexicmap lexicmap_index, lexicmap_search LexicMap is a nucleotide sequence alignment tool for efficiently querying genomes. 2025-06-16 https://github.com/shenwei356/LexicMap 0.8.0 lexicmap 0.8.0 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap lexicmap LexicMap LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline 2017-05-24 http://bioconductor.org/packages/release/bioc/html/limma.html 3.58.1 bioconductor-limma 3.62.1 To update Transcriptomics, RNA, Statistics RNA-Seq analysis RNA-Seq analysis Molecular biology, Genetics Molecular biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom limma limma Data analysis, linear models and differential expression for microarray data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2902 3166 27013 30001 5247 6265 50381 59995 921 1003 10130 11326 26 26 329 329 101651 87853 10460 9096 https://usegalaxy.eu/published/workflow?id=09c77b6fc5add851, https://usegalaxy.eu/published/workflow?id=14226641bba951f3, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1c1083b159e5bfb2, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=263eed267aa3e76b, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2ecf737b53f77cf8, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=47f2c44d79896f08, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=7036a6cf67d53bc7, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=8ab363878cd34ef0, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=8f095e5b9594b098, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=ad3be77eb2e8c10e, https://usegalaxy.eu/published/workflow?id=bb4ecac751a94c79, https://usegalaxy.eu/published/workflow?id=c8deb8952abce1ec, https://usegalaxy.eu/published/workflow?id=d6eb0562d0036940, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0a009cf9e88171f1, https://usegalaxy.org/published/workflow?id=0c052e50594f6d2d, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=204d0da8a023d7da, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/689?version=1 transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes
lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) 2023-07-04 https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html 1.6.0 r-base To update Metagenomics, Sequence Analysis Variant calling Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 39 39 0 0 0 0 0 0 0 0 0 0 0 0 39 39 4 4
links links Scaffold genome assemblies with long reads. 2022-02-23 https://github.com/bcgsc/LINKS 2.0.1 links 2.0.1 Up-to-date Assembly Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 181 181 940 940 0 0 0 0 87 87 778 778 0 0 0 0 1718 1718 268 268
lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. 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longdust longdust Detect low-complexity regions in long DNA sequences using k-mer statistics. 2025-10-01 https://github.com/lh3/longdust 1.2 longdust 1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lorikeet_spoligotype lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 2018-05-07 https://github.com/AbeelLab/lorikeet 20 lorikeet 20 Up-to-date Sequence Analysis Sequence analysis, Genotyping Sequence analysis, Genotyping Genotype and phenotype Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 930 930 0 0 0 0 0 0 0 0 0 0 0 0 930 930 18 18
lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery 2020-11-12 https://github.com/arq5x/lumpy-sv 0.3.1 lumpy-sv 0.3.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 139 139 2586 2586 0 0 0 0 0 0 0 0 0 0 0 0 2586 2586 139 139 https://usegalaxy.eu/published/workflow?id=3d8aa05129e44fdf
m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data 2023-10-25 https://m6anet.readthedocs.io/en/latest 2.1.0 m6anet 2.1.0 Up-to-date Sequence Analysis Quantification, Imputation, Gene expression profiling Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning RNA-Seq, Transcriptomics, RNA, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 12 12 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 12 12
maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. 2021-11-05 http://huttenhower.sph.harvard.edu/maaslin 1.18.0 bioconductor-maaslin2 1.18.0 Up-to-date Metagenomics Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Metagenomics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 100 100 3676 3676 0 0 0 0 0 0 0 0 2 2 4 4 3680 3680 102 102 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962
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https://usegalaxy.org/published/workflow?id=fce1837144d3a86e, https://usegalaxy.org/published/workflow?id=fd75347cfea06651, https://usegalaxy.org/published/workflow?id=fda29ba2b6c98f8b, https://usegalaxy.org/published/workflow?id=fe2d15d352a9919f, https://usegalaxy.org/published/workflow?id=fe4c2791508c56ab, https://usegalaxy.org/published/workflow?id=fff1a5c7475b3eeb, https://workflowhub.eu/workflows/1506?version=1, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1568?version=1, https://workflowhub.eu/workflows/1606?version=1, https://workflowhub.eu/workflows/1615?version=1, https://workflowhub.eu/workflows/1620?version=1, https://workflowhub.eu/workflows/395?version=15, https://workflowhub.eu/workflows/397?version=15, https://workflowhub.eu/workflows/398?version=16, https://workflowhub.eu/workflows/399?version=19, https://workflowhub.eu/workflows/561?version=11 epigenetics/atac-seq, epigenetics/cut_and_run, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, epigenetics/tal1-binding-site-identification, single-cell/scatac-preprocessing-tenx
maf_stats maf_stats1 MAF Coverage statistics 2020-08-12 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1 1 1 1 0 1 0 0 0 1 0 0 0 1 1 1 0 1 0 0 0 1 1 0 0 0 0 1 0 1 1 1 1 5 9 9 21 47 469 176 2482 1 1 1 1 0 0 0 0 2504 186 479 53
maf_tools ucsc_mafaddirows, ucsc_mafcoverage, ucsc_maffetch, ucsc_mafFilter, ucsc_maffrag, ucsc_maffrags Utilities for working with MAF (Multiple Alignment Format) files from UCSC 2025-06-03 http://genome.ucsc.edu 482 ucsc-mafaddirows 482 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 2017-11-08 https://sourceforge.net/projects/mageck/ 0.5.9.2 mageck 0.5.9.5 To update Genome editing Genetic variation analysis Genetic variation analysis Genetics, Genetic variation, Genomics Genetics, Genetic variation, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 407 423 13575 15010 433 433 13443 13443 137 139 6643 7099 5 5 41 41 35593 33702 1000 982 https://workflowhub.eu/workflows/1534?version=1 genome-annotation/crispr-screen
magicblast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome 2022-04-05 https://ncbi.github.io/magicblast/ 1.7.0 magicblast 1.7.0 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 230 230 8803 8803 0 0 0 0 1 1 2 2 0 0 0 0 8805 8805 231 231
maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.04 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1323 1455 7332 8835 1701 1808 9536 10359 904 904 4968 4989 33 33 211 211 24394 22047 4200 3961 https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1 genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short
malt_run malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. 2021-11-12 https://github.com/husonlab/malt 0.5.3 malt 0.62 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 27 27 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9
map_damage map_damage Tracks and quantifies specific ancient DNA damage patterns for authentication. 2025-06-27 https://ginolhac.github.io/mapDamage/ 2.2.3 mapdamage2 2.2.3 Up-to-date Sequence Analysis, Statistics, Visualization Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage mapdamage MapDamage Identify and quantify DNA damage patterns in ancient DNA. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 36 36 0 0 0 0 0 0 0 0 2 2 3 3 39 39 5 5
map_param_value map_param_value Map a parameter value to another value 2022-10-13 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 6460 6460 216 216 5530 5530 10 10 321 321 4 4 30 30 12341 12341 393 393 https://usegalaxy.eu/published/workflow?id=0603f0898211f806, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=0eb137cd936bbfe0, https://usegalaxy.eu/published/workflow?id=18af9bbae833f8fe, https://usegalaxy.eu/published/workflow?id=249c5d6698c8b98c, https://usegalaxy.eu/published/workflow?id=2d08a73dd8ff99e9, https://usegalaxy.eu/published/workflow?id=373d861ef4b0081a, https://usegalaxy.eu/published/workflow?id=406e6ef0dfb38628, https://usegalaxy.eu/published/workflow?id=409336bf210033a2, 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maplot maplot Generate MA plots for visualizing data distributions using Plotly or Matplotlib. 2025-04-17 https://github.com/galaxyproject/tools-iuc 1.0.0 plotly To update Visualization, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/maplot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq 2.1.1b perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 9612 9612 24 24 434 434 0 0 0 0 0 0 0 0 10046 10046 88 88 https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1 microbiome/mgnify-amplicon
mash mash_dist, mash_paste, mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash 2018-12-07 https://github.com/marbl/Mash 2.3 mash 2.3 Up-to-date Metagenomics Sequence distance matrix generation Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash mash Mash Fast genome and metagenome distance estimation using MinHash. 4 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 49 57 10768 10867 18 18 922 922 18 18 3187 3187 3 3 29 29 15005 14906 96 88
mashmap mashmap Fast local alignment boundaries 2024-02-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap 3.1.3 mashmap 3.1.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 33 1329 1329 35 35 1094 1094 0 0 0 0 0 0 0 0 2423 2423 68 68 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5aaa64ecdf9f7d6e, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=f9a73b39b2051af1
masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments 2017-05-09 https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html 1.49.3 coreutils 8.25 To update Transcriptomics, RNA, Statistics Regression analysis Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq Gene expression, Microarray experiment, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 200 628 75 88 522 630 0 0 0 0 0 0 0 0 1258 722 132 110
maxbin2 maxbin2 clusters metagenomic contigs into bins 2019-10-24 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html maxbin2 2.2.7 To update Metagenomics Sequence assembly Sequence assembly Metagenomics, Sequence assembly, Microbiology Metagenomics, Sequence assembly, Microbiology mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 408 433 5244 5537 634 675 2694 2993 106 108 1135 1198 6 6 648 648 10376 9721 1222 1154 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1352?version=3
mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs 2022-05-12 https://micans.org/mcl/man/mcl.html 22.282 mcl 22.282 Up-to-date Sequence Analysis Clustering, Network analysis, Gene regulatory network analysis Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 18 153 153 0 0 0 0 0 0 0 0 0 0 0 0 153 153 18 18
medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 1.7.2 medaka 2.1.1 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 1728 1734 155538 156220 735 735 76698 76698 421 421 11622 11622 17 17 2659 2659 247199 246517 2907 2901 https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4d97068a725c975c, https://usegalaxy.eu/published/workflow?id=529f30e894beacc2, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=7bdd9ad918edab0b, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=b97532c398b821a2, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.fr/published/workflow?id=61235264d5d2f666, https://usegalaxy.fr/published/workflow?id=727cfdb7c79287d1, https://usegalaxy.fr/published/workflow?id=e3c04a30258421aa, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=0c6f7bfc826433c4, https://usegalaxy.org.au/published/workflow?id=47ce6a2d30887637, https://usegalaxy.org.au/published/workflow?id=48a60965b6b3ff54, https://usegalaxy.org.au/published/workflow?id=4bc8ac41ecff7daf, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=705658f68ae73930, https://usegalaxy.org.au/published/workflow?id=888f8377eb6eabf2, https://usegalaxy.org.au/published/workflow?id=932bad88f8dc8d33, https://usegalaxy.org.au/published/workflow?id=ba7a9d4c857d26b7, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=4357180d40560019, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=88d0b64011c3148c, https://usegalaxy.org/published/workflow?id=953d9cbe05e632a8, https://usegalaxy.org/published/workflow?id=9adf8691809326e5, https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114, https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3428dd172a78102, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1578?version=1, https://workflowhub.eu/workflows/226?version=1 assembly/largegenome, microbiome/pathogen-detection-from-nanopore-foodborne-data
megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 2017-09-22 https://github.com/voutcn/megahit 1.2.9 megahit 1.2.9 Up-to-date Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 2052 2197 22340 24371 2823 2929 23973 24874 615 632 9338 9643 54 54 1387 1387 60275 57038 5812 5544 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7d84b0419296857d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1, https://workflowhub.eu/workflows/1634?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly, microbiome/metagenomics-binning
megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) 2018-11-09 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp 1.1.3 megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 200 212 763 862 113 113 338 338 33 33 150 150 6 6 80 80 1430 1331 364 352 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1634?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). 2021-11-24 https://github.com/husonlab/megan-ce 6.21.7 megan 6.25.10 To update Sequence Analysis Sequence analysis, Taxonomic classification Sequence analysis, Taxonomic classification Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. 0 1 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 250 250 5164 5164 0 0 0 0 5 5 72 72 3 3 4 4 5240 5240 258 258
meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen, meme_streme The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. 2015-12-13 http://meme-suite.org/ 5.5.8 meme 5.5.8 Up-to-date ChIP-seq Sequence motif discovery, Sequence motif recognition, Sequence motif comparison, Transcriptional regulatory element prediction Sequence motif discovery, Sequence motif recognition, Sequence motif comparison, Transcriptional regulatory element prediction Sequence sites, features and motifs, ChIP-seq, RNA immunoprecipitation, Epigenetics, Small molecules Sequence sites, features and motifs, ChIP-seq, RNA immunoprecipitation, Epigenetics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme streme STREME STREME is accurate and versatile sequence motif discovery tool. The MEME Suite allows you to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (STREME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). MEME-ChIP performs a comprehensive motif-based analysis of ChIP-seq and other large sequence datasets. 3 0 5 0 0 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 476 632 6756 24611 1135 2866 9050 27707 0 0 0 0 0 2 0 150 52468 15806 3500 1611 https://usegalaxy.org/published/workflow?id=2049d38325423cfe, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab
meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. 2018-03-15 http://meme-suite.org/ 4.11.2 graphicsmagick 1.3.26 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 724 899 6897 8466 1240 1394 7722 8507 0 0 0 0 0 0 0 0 16973 14619 2293 1964 https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.org/published/workflow?id=59d34b4f0178120b, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1706?version=1 epigenetics/cut_and_run, transcriptomics/clipseq
meningotype meningotype Assign sequence type to N. meningitidis genome assemblies 2023-06-06 https://github.com/MDU-PHL/meningotype 0.8.5 meningotype 0.8.5 Up-to-date Sequence Analysis Genotyping, Multilocus sequence typing Multilocus sequence typing Microbiology, Genotype and phenotype Microbiology, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
merlin merlin Pedigree Analysis package 2020-04-15 http://csg.sph.umich.edu/abecasis/Merlin/ 1.1.2 merlin 1.1.2 Up-to-date Variant Analysis Haplotype mapping, Genetic mapping Haplotype mapping GWAS study, Mapping GWAS study, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. 2021-04-18 https://github.com/marbl/merqury 1.3 merqury 1.3 Up-to-date Assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Sequence assembly, Whole genome sequencing, Plant biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 661 661 4657 4657 264 264 1645 1645 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merquryfk merquryfk_asmplot, merquryfk_cnplot, merquryfk_hapmaker, merquryfk_happlot, merquryfk_merquryfk FastK based version of Merqury 2025-02-11 https://github.com/thegenemyers/MERQURY.FK 1.1.1 merquryfk 1.1.3 To update Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. 2021-04-05 https://github.com/marbl/meryl 1.3 merqury 1.3 Up-to-date Assembly k-mer counting k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Whole genome sequencing, Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 55 1850 1850 77 77 1478 1478 0 0 0 0 0 0 0 0 3328 3328 132 132 https://usegalaxy.eu/published/workflow?id=0ccb3838765a8b84, https://usegalaxy.eu/published/workflow?id=10bde4e7f8dbd0c4, https://usegalaxy.eu/published/workflow?id=41c48e4632684f76, https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://usegalaxy.org/published/workflow?id=9f1aabc6f5d18d13, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://usegalaxy.org/published/workflow?id=beefb67de2b0728c, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/632?version=12
metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. 2022-01-28 https://bitbucket.org/berkeleylab/metabat/src/master/ 2.17 metabat2 2.18 To update Metagenomics Read binning, Sequence assembly, Genome annotation Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Metagenomics, Sequence assembly, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 MetaBAT_2 MetaBAT 2 an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 670 670 14194 14194 375 375 2591 2591 167 167 1738 1738 18 18 1359 1359 19882 19882 1230 1230 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3
metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences 2024-06-04 https://github.com/steineggerlab/Metabuli 1.0.5 metabuli 1.1.0 To update Sequence Analysis, Metagenomics Taxonomic classification Taxonomic classification Taxonomy Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 2020-08-04 https://github.com/soedinglab/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 To update Sequence Analysis, Genome annotation Homology-based gene prediction Homology-based gene prediction Metagenomics, Gene and protein families Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 58 507 509 0 0 0 0 0 0 0 0 0 0 0 0 509 507 58 57 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92
metagenomeseq_normalization metagenomeseq_normalizaton metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 23 521 763 28 56 261 530 0 0 0 0 0 0 0 0 1293 782 79 43
metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.1.1 metaphlan 4.2.3 To update Metagenomics Taxonomic classification, Taxonomic classification Taxonomic classification, Taxonomic classification Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. 1 2 4 4 0 0 0 0 0 0 0 0 0 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 0 1552 1552 30934 31014 1122 1122 20021 20021 314 314 6347 6347 28 28 211 211 57593 57513 3016 3016 https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=1, https://workflowhub.eu/workflows/624?version=1 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling
metasbt metasbt_index, metasbt_profile Microbial genomes characterization with Sequence Bloom Trees 2025-08-22 https://github.com/cumbof/MetaSBT 0.1.5 sed To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
metawrapmg_binning metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis 2024-04-11 https://github.com/bxlab/metaWRAP 1.3.0 metawrap-mg 1.3.0 Up-to-date Metagenomics Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Whole genome sequencing, Metagenomic sequencing, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 100 1596 1596 0 0 0 0 67 67 587 587 0 0 0 0 2183 2183 167 167
mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2024-07-12 https://github.com/EBI-Metagenomics/emg-toolkit 0.10.4 mg-toolkit 0.10.4 Up-to-date Metagenomics Data retrieval Data retrieval Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 21 21 0 0 0 0 0 0 0 0 0 0 0 0 21 21 10 10
micro_decon micro_decon An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing 2025-08-05 https://github.com/donaldtmcknight/microdecon 1.0.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
microsatbed microsatbed Select microsatellites for a bed file 2024-07-21 https://github.com/lmdu/pytrf 1.3.3 python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 949 949 20 20 740 740 0 0 0 0 0 0 0 0 1689 1689 36 36 https://usegalaxy.eu/published/workflow?id=3b94f511c52da835
migmap migmap mapper for full-length T- and B-cell repertoire sequencing 2017-09-29 https://github.com/mikessh/migmap 1.0.3 migmap 1.0.3 Up-to-date RNA, Sequence Analysis Sequence analysis, Read mapping Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24 39 931 1301 73 101 1138 1564 0 0 0 0 0 0 0 0 2865 2069 140 97
minia minia Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ 3.2.6 minia 3.2.6 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 272 287 6758 7224 0 0 0 0 77 77 357 357 0 0 0 0 7581 7115 364 349 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40
miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm 0.3_r179 miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 571 687 11506 14702 474 538 9124 10016 88 96 1235 1277 16 16 166 166 26161 22031 1337 1149 https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore
minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences 2017-11-03 https://github.com/lh3/minimap2 2.28 minimap2 2.30 To update Next Gen Mappers Pairwise sequence alignment Pairwise sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5844 6182 414670 442793 5535 5834 153408 159247 1454 1492 29827 30676 169 170 4829 4841 637557 602734 13678 13002 https://usegalaxy.eu/published/workflow?id=032a7281a86eba0d, https://usegalaxy.eu/published/workflow?id=03bb4c20a1f4b4de, https://usegalaxy.eu/published/workflow?id=0444c98a3ca2a3ca, https://usegalaxy.eu/published/workflow?id=04844dddcc4e8aa7, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, 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miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.18 miniprot 0.18 Up-to-date Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 100 100 5038 5038 42 42 364 364 0 0 0 0 25 25 283 283 5685 5685 167 167 https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe
mirmachine mirmachine Tool to detect miRNA in genome sequences 2024-03-15 https://github.com/sinanugur/MirMachine 0.3.0.1 mirmachine 0.3.0.1 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10
mirnature mirnature Computational detection of canonical microRNAs 2022-12-11 https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 Up-to-date RNA, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 23 23 0 0 0 0 0 0 0 0 0 0 0 0 23 23 11 11
mitobim mitobim assemble mitochondrial genomes 2020-12-29 https://github.com/chrishah/MITObim 1.9.1 mitobim 1.9.1 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 168 168 1463 1463 0 0 0 0 39 39 533 533 0 0 0 0 1996 1996 207 207
mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ 1.1.7 mitos 2.1.9 To update Sequence Analysis Genome annotation Genome annotation Zoology, Whole genome sequencing Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 1326 1336 267673 268177 772 772 84561 84561 151 151 15492 15492 6 6 109 109 368339 367835 2265 2255 https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10
mlst mlst, mlst_list Scan contig files against PubMLST typing schemes 2016-12-12 https://github.com/tseemann/mlst 2.22.0 mlst 2.23.0 To update Sequence Analysis Multilocus sequence typing Multilocus sequence typing Immunoproteins and antigens Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1786 1918 24365 26341 1356 1420 12903 13604 1137 1439 12595 15564 22 22 99 99 55608 49962 4799 4301 https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be microbiome/pathogen-detection-from-nanopore-foodborne-data
mmseqs2 mmseqs2_easy_linclust_clustering, mmseqs2_taxonomy_assignment MMseqs2 is an ultra fast and sensitive sequence search and clustering suite 2025-03-27 https://github.com/soedinglab/MMseqs2 17-b804f mmseqs2 17.b804f To update Sequence Analysis, Metagenomics Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Metagenomics, Sequence analysis, Proteins, Nucleic acids, Gene and protein families, Taxonomy Metagenomics, Sequence analysis, Nucleic acids, Gene and protein families, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 MMseqs2 MMseqs2 MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 260 260 0 0 0 0 0 0 0 0 3 3 29 29 289 289 45 45
mmuphin mmuphin MMUPHin is an R package implementing meta-analysis methods for microbial community profiles 2024-11-22 https://huttenhower.sph.harvard.edu/mmuphin 1.16.0 bioconductor-mmuphin 1.16.0 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin mmuphin mmuphin MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 14 14 0 0 0 0 0 0 0 0 0 0 0 0 14 14 3 3 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264
moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. 2019-07-28 https://github.com/sunnyisgalaxy/moabs 1.3.4.6 moabs 1.3.9.6 To update Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46 59 185 351 0 0 0 0 0 0 0 0 0 0 0 0 351 185 59 46
mosdepth mosdepth fast and flexible BAM/CRAM depth calculation 2022-12-04 https://github.com/brentp/mosdepth 0.3.11 mosdepth 0.3.11 Up-to-date SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 201 201 14592 14592 173 173 13590 13590 73 73 3292 3292 1 1 1500 1500 32974 32974 448 448 https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://usegalaxy.org/published/workflow?id=0c6dbb2ef5eee5b9, https://usegalaxy.org/published/workflow?id=695d20ef3ee4cf1e, https://usegalaxy.org/published/workflow?id=779ea0b19d07a1bd, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1647?version=1 variant-analysis/tb-variant-analysis
mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers 2016-06-24 https://www.mothur.org 1.0 mothur 1.48.3 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Microbial ecology, Taxonomy, Sequence analysis, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities 129 129 129 129 0 0 0 0 0 0 0 0 0 0 129 0 3 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 2291 2805 265024 361038 4027 5455 423935 750968 1447 1742 164152 213607 147 149 14583 14948 1340561 867694 10151 7912 https://usegalaxy.eu/published/workflow?id=565c989730f68362, https://usegalaxy.eu/published/workflow?id=6d06bd22f206e176, https://usegalaxy.eu/published/workflow?id=6efd80daabf518bf, https://usegalaxy.eu/published/workflow?id=7783eeebfa264bf5, https://usegalaxy.eu/published/workflow?id=83a0c1ba280785e6, 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msaboot msaboot A multiple sequences alignment bootstrapping tool. 2018-02-12 https://github.com/phac-nml/msaboot 0.1.2 msaboot 0.1.2 Up-to-date Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 109 131 1009 1133 199 228 1049 1320 0 0 0 0 0 0 0 0 2453 2058 359 308
multigps multigps Analyzes collections of multi-condition ChIP-seq data. 2017-03-06 http://mahonylab.org/software/multigps/ 0.74.0 fonts-conda-ecosystem To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 121 304 317 891 0 0 0 0 0 0 0 0 892 318 305 122
multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data 2023-06-07 https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html 1.12.0 bioconductor-multigsea 1.16.0 To update Transcriptomics, Proteomics, Statistics, Single Cell Gene-set enrichment analysis, Aggregation, Pathway analysis Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 65 65 212 212 0 0 0 0 5 5 46 46 0 0 0 0 258 258 70 70 https://workflowhub.eu/workflows/1388?version=1 proteomics/multiGSEA-tutorial
multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report 2017-09-21 http://multiqc.info/ 1.27 multiqc 1.31 To update Fastq Manipulation, Statistics, Visualization Validation, Sequencing quality control Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics Sequencing, Bioinformatics, Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. 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transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis
mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools 2018-06-28 https://github.com/mummer4/mummer 4.0.0 mummer4 4.0.1 To update Sequence Analysis Multiple sequence alignment Multiple sequence alignment Sequence analysis, Human genetics Sequence analysis, Human genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 842 940 30656 33196 1586 1727 32334 36481 295 295 12782 12782 21 21 595 595 83054 76367 2983 2744 https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=35629b113a6f23ab, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef, https://usegalaxy.org/published/workflow?id=8b4b62a55a93a258
muon cluster_analyze_embed_muon, mudata_import_export, plot_muon, preprocess_muon muon is a Python framework for multimodal omics analysis 2024-03-15 https://muon.readthedocs.io 0.1.6 muon To update Single Cell, Sequence Analysis, Transcriptomics, Epigenetics Cell biology, Single-cell sequencing, Gene expression, Epigenetics, Multiomics Cell biology, Gene expression, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon muon muon muon is a Python framework for multimodal omics analysis. 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mykrobe mykrobe_predict Antibiotic resistance predictions 2017-12-18 https://github.com/Mykrobe-tools/mykrobe 0.10.0 mykrobe 0.13.0 To update Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzmine_batch mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data 2023-10-21 http://mzmine.github.io/ 3.9.0 mzmine 4.7.29 To update Metabolomics Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Proteomics, Metabolomics, Proteomics experiment, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 21 21 0 0 0 0 0 0 0 0 0 0 0 0 21 21 8 8
naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) 2022-04-11 https://github.com/BlankenbergLab/nAltORFs 0.1.2 naltorfs 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60 60 271 271 0 0 0 0 0 0 0 0 271 271 60 60
nanocomp nanocomp Compare multiple runs of long read sequencing data and alignments 2025-05-21 https://github.com/wdecoster/NanoComp 1.25.3 nanocomp 1.25.4 To update Visualization, Statistics, Fastq Manipulation Box-Whisker plot plotting, Visualisation, Multiple sample visualisation Box-Whisker plot plotting, Multiple sample visualisation Nucleic acids, Bioinformatics Nucleic acids, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp nanocomp nanocomp Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2
nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. 2020-04-27 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5 7 27 839 0 0 0 0 5 5 365 371 0 0 0 0 1210 392 12 10 https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d
nanoplot nanoplot Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot 1.46.1 nanoplot 1.46.1 Up-to-date Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 7663 7942 168514 173861 4903 5029 72856 74900 2940 2983 25741 26566 295 297 3814 3828 279155 270925 16251 15801 https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, 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nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. 2020-04-27 https://a-slide.github.io/NanopolishComp 0.6.11 nanopolishcomp 0.6.12 To update Sequence Analysis Methylation analysis, Collapsing methods Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation Sequence analysis, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 36 38 709 1129 0 0 0 0 0 0 0 0 1 1 1 1 1130 710 39 37 https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d
ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2019-11-06 https://github.com/kblin/ncbi-acc-download 0.2.8 ncbi-acc-download 0.2.8 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2027 2167 9533 10236 4656 5221 17731 19952 1153 1204 6985 7379 47 49 329 345 37912 34578 8641 7883 https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=4d80a87510b2a54e, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f, https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2cbcfeb772f348c9, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://workflowhub.eu/workflows/1558?version=1, https://workflowhub.eu/workflows/1628?version=1 genome-annotation/secondary-metabolite-discovery, variant-analysis/baculovirus-isolate-variation
ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. 2022-01-27 https://github.com/ncbi/datasets 18.5.1 ncbi-datasets-cli To update Data Source Data handling, Sequence database search, Data retrieval Data handling, Sequence database search, Data retrieval Biological databases Biological databases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 1310 1310 6574 6574 3022 3022 17889 17889 2 2 3 3 88 88 425 425 24891 24891 4422 4422 https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 genome-annotation/bacterial-comparative-genomics-dataset-construction
ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases 2022-03-22 http://www.ncbi.nlm.nih.gov/books/NBK179288/ 22.4 entrez-direct 24.0 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 0 0 0 0 0 0 0 0 3 0 1 0
ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases 2015-04-14 https://www.ncbi.nlm.nih.gov/books/NBK25501/ 1.70 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 2 0 0 0 0 0 0 0 7 7 0 242 422 2452 3350 0 0 0 0 0 0 0 0 0 0 0 0 3350 2452 422 242
ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). 2023-09-21 https://github.com/ncbi/fcs-gx 0.5.5 ncbi-fcs-gx 0.5.5 Up-to-date Sequence Analysis Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Sequence analysis, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 175 175 2259 2259 485 485 26859 26859 27 27 955 955 1 1 9 9 30082 30082 688 688 https://usegalaxy.org/published/workflow?id=927b8f90ad9603a7, https://workflowhub.eu/workflows/645?version=14 sequence-analysis/ncbi-fcs
necat necat Error correction and de-novo assembly for ONT Nanopore reads 2021-11-29 https://github.com/xiaochuanle/NECAT 0.0.1_update20200803 necat 0.0.1_update20200803 Up-to-date Assembly De-novo assembly De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 228 228 1106 1106 0 0 0 0 0 0 0 0 0 0 0 0 1106 1106 228 228
newick_utils newick_display Perform operations on Newick trees 2018-10-01 https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 To update Visualization, Metagenomics Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science Phylogeny, Genomics, Computer science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1756 1893 51682 53373 2196 2332 18983 20195 1114 1145 9635 9912 48 49 310 312 83792 80610 5419 5114 https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1418?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/653?version=1 evolution/abc_intro_phylo, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data
nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain 2021-03-29 https://github.com/nextstrain/nextclade 2.7.0 nextalign 2.14.0 To update Sequence Analysis Methylation analysis, Variant calling Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics Genomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 373 373 4718 4718 309 309 11632 11632 258 258 2460 2460 11 11 723 723 19533 19533 951 951 https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/155?version=6, https://workflowhub.eu/workflows/520?version=1 variant-analysis/sars-cov-2-variant-discovery
ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads 2020-10-27 https://github.com/philres/ngmlr 0.2.7 ngmlr 0.2.7 Up-to-date Next Gen Mappers DNA mapping, Sequence alignment, Genetic variation analysis DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 53 53 1408 1408 0 0 0 0 0 0 0 0 0 0 0 0 1408 1408 53 53 https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5
ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. 2015-11-10 https://github.com/ngsutils/ngsutils ngsutils 0.5.9 To update SAM Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 702 894 27862 37369 902 1390 17094 25161 128 176 10945 13368 21 21 148 148 76046 56049 2481 1753 https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=a7726d18d2a5fcf2, https://usegalaxy.org/published/workflow?id=18899840e49d89c3, https://usegalaxy.org/published/workflow?id=1f48b44fa22ac5fc, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly
nonpareil nonpareil Estimate average coverage in metagenomic datasets 2017-11-03 http://nonpareil.readthedocs.io 3.5.5 nonpareil 3.5.5 Up-to-date Metagenomics Operation Operation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 19 105 195 23 26 122 168 0 0 0 0 0 0 0 0 363 227 45 39
novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. 2020-05-18 https://github.com/ndierckx/NOVOPlasty 4.3.1 novoplasty 4.3.5 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 502 502 11073 11073 1 1 1 1 137 137 3542 3542 11 11 37 37 14653 14653 651 651 https://usegalaxy.eu/published/workflow?id=5436eb1c430a38dd
nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. 2016-11-18 https://github.com/tecangenomics/nudup 2.3.3 nudup 2.3.3 Up-to-date SAM, Metagenomics, Sequence Analysis, Transcriptomics Duplication detection, Sequence analysis Duplication detection, Sequence analysis Sequencing, Genomics Sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 http://metabarcoding.org/obitools 1.2.13 obitools 1.2.13 Up-to-date Sequence Analysis Sequence analysis, Sequence analysis Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Sequence analysis, DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 483 493 45330 45705 0 0 0 0 107 107 5011 5011 25 25 1398 1398 52114 51739 625 615 https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 ecology/Obitools-metabarcoding
ococo ococo Variant detection of SNVs 2017-12-07 https://github.com/karel-brinda/ococo 0.1.2.6 ococo 0.1.2.7 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 71 101 1253 2070 186 208 1426 1552 0 0 0 0 0 0 0 0 3622 2679 309 257 https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df
odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. 2020-04-06 https://github.com/vgteam/odgi 0.3 odgi 0.9.3 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3 4 7 29 0 0 0 0 0 0 0 0 0 0 0 0 29 7 4 3
omark omark Proteome quality assessment software 2023-11-15 https://github.com/DessimozLab/OMArk 0.3.1 To update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 89 89 707 707 17 17 44 44 6 6 11 11 15 15 347 347 1109 1109 127 127 https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1096?version=2, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1746?version=1 genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer
ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. 2020-06-08 https://github.com/nanoporetech/ont_fast5_api/ 3.1.3 ont-fast5-api 4.1.3 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 49 51 2529 3106 0 0 0 0 0 0 0 0 0 0 0 0 3106 2529 51 49 https://usegalaxy.eu/published/workflow?id=d5b1fab611ddfeb0, https://usegalaxy.eu/published/workflow?id=e271d95a671182ec
onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. 2017-11-04 http://search.cpan.org/~easr/ONTO-PERL-1.45/ 1.45 perl-onto-perl 1.45 Up-to-date Ontology Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 8 11 75 666 0 0 0 0 0 0 0 0 0 0 0 0 666 75 11 8
openalex_explorer openalex_explorer Fetch citing papers from OpenAlex using DOI, ID and title 2025-05-29 https://openalex.org/ 0.1.0+galaxy0 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/openalex https://github.com/galaxyproject/tools-iuc/tree/main/tools/openalex 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 8 8 0 0 0 0 0 0 0 0 0 0 0 0 8 8 3 3
optdoe optdoe Optimal Design Of Experiment 2022-10-27 https://github.com/pablocarb/doebase v2.0.2 doebase To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
optitype optitype Precision HLA typing from NGS data 2021-02-17 https://github.com/FRED-2/OptiType 1.3.5 optitype 1.3.5 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 62 62 585 585 18 18 99 99 6 6 97 97 0 0 0 0 781 781 86 86 https://usegalaxy.eu/published/workflow?id=db270d0eb035609e, https://usegalaxy.org.au/published/workflow?id=2249ab6710f5e84d, https://usegalaxy.org/published/workflow?id=1d925422fc6094a0, https://workflowhub.eu/workflows/1430?version=1, https://workflowhub.eu/workflows/1794?version=1 proteomics/neoantigen-predicting-hla-binding
orfipy orfipy Galaxy wrapper for ORFIPY 2022-04-07 https://github.com/urmi-21/orfipy 0.0.4 orfipy 0.0.4 Up-to-date Sequence Analysis Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Computer science, RNA-Seq, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 1509 1509 343 343 2776 2776 0 0 0 0 0 0 0 0 4285 4285 515 515 https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df genome-annotation/gene-centric
orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy 2017-05-22 https://github.com/davidemms/OrthoFinder 2.5.5 orthofinder 3.1.0 To update Phylogenetics, Sequence Analysis Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 801 801 3870 3870 0 0 0 0 133 133 1450 1450 36 36 221 221 5541 5541 970 970
packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection 2022-01-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader 0.1 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. 2024-08-13 https://github.com/BioinformaticsPlatformWIV-ISP/PACU 0.0.5 pacu_snp 0.0.7 To update Sequence Analysis, Phylogenetics Clustering Clustering Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 223 223 0 0 0 0 0 0 0 0 0 0 0 0 223 223 19 19
pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing 2024-03-26 https://pairtools.readthedocs.io 1.1.3 pairtools 1.1.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 742 742 8 8 415 415 0 0 0 0 0 0 0 0 1157 1157 33 33 https://usegalaxy.org/published/workflow?id=3a92253f57e553bd, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/625?version=27
panaroo panaroo A Bacterial Pangenome Analysis Pipeline 2025-02-28 https://gthlab.au/panaroo/#/ 1.5.2 panaroo 1.5.2 Up-to-date Sequence Analysis De-novo assembly, Genome assembly, Clustering De-novo assembly, Genome assembly, Clustering Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo panaroo Panaroo Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 67 297 297 0 0 0 0 39 39 312 312 0 0 0 0 609 609 106 106
pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. 2021-03-06 https://github.com/cov-lineages/pangolin 4.3 pangolin 4.3.1 To update Sequence Analysis Tree-based sequence alignment, Variant classification Tree-based sequence alignment, Variant classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 595 595 7737 7737 416 416 9068 9068 277 277 3099 3099 12 12 603 603 20507 20507 1300 1300 https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/1391?version=1, https://workflowhub.eu/workflows/155?version=6 galaxy-interface/workflow-automation, variant-analysis/sars-cov-2-variant-discovery
panta panta Efficient inference of large prokaryotic pangenomes with PanTA. 2025-09-15 https://github.com/amromics/panta 1.0.1 panta 1.0.1 Up-to-date Genome annotation, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. 2022-05-12 https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py 1.0.2 parse_mito_blast 1.0.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 136 136 1872 1872 95 95 1193 1193 33 33 178 178 0 0 0 0 3243 3243 264 264 https://usegalaxy.eu/published/workflow?id=012762cb4acb068b, https://usegalaxy.eu/published/workflow?id=0f044c9f62773a88, https://usegalaxy.eu/published/workflow?id=10150b1a188f6d07, https://usegalaxy.eu/published/workflow?id=12a018217ee146ca, https://usegalaxy.eu/published/workflow?id=2497292e98937a5f, https://usegalaxy.eu/published/workflow?id=2c2f0b4312bae4f4, https://usegalaxy.eu/published/workflow?id=33a052f9a3d5551d, https://usegalaxy.eu/published/workflow?id=3dec7c9b02c3d1ee, https://usegalaxy.eu/published/workflow?id=8a14cda6140acab7, https://usegalaxy.eu/published/workflow?id=8c7e972020799d57, https://usegalaxy.eu/published/workflow?id=8d64614d1971065a, https://usegalaxy.eu/published/workflow?id=9588311136ac8794, https://usegalaxy.eu/published/workflow?id=c4fc3adf8f7ff2bc, https://usegalaxy.eu/published/workflow?id=ec6b2c926fffab5f, https://usegalaxy.org.au/published/workflow?id=0edb9c8b767fa74b, https://usegalaxy.org.au/published/workflow?id=29ce205d98faf47e, https://usegalaxy.org.au/published/workflow?id=3d47e0de658b3304, https://usegalaxy.org.au/published/workflow?id=4047f9f242542716, https://usegalaxy.org.au/published/workflow?id=5fb44f257e445f56, https://usegalaxy.org.au/published/workflow?id=8034bd0690b4cbe8, https://usegalaxy.org.au/published/workflow?id=83441e3de699d157, https://usegalaxy.org.au/published/workflow?id=897a1255cef5c310, https://usegalaxy.org.au/published/workflow?id=97e55a900db3863b, https://usegalaxy.org.au/published/workflow?id=c92fead7c30c7497, https://usegalaxy.org.au/published/workflow?id=d2dcd3b54e5082a6, https://usegalaxy.org.au/published/workflow?id=d417e920ff97e4c1, https://usegalaxy.org.au/published/workflow?id=d720c98f7227b6d5, https://usegalaxy.org/published/workflow?id=1473cdcbd664d147, https://usegalaxy.org/published/workflow?id=1b80302437db5937, https://usegalaxy.org/published/workflow?id=5c259623a010fe77, https://usegalaxy.org/published/workflow?id=5e38c7b36e4918ad, https://usegalaxy.org/published/workflow?id=605160c81d098703, https://usegalaxy.org/published/workflow?id=7c9a55db0b0eb178, https://usegalaxy.org/published/workflow?id=927b8f90ad9603a7, https://usegalaxy.org/published/workflow?id=b7fe3873ee5e3a02, https://usegalaxy.org/published/workflow?id=c8f9e048ddae7d03, https://usegalaxy.org/published/workflow?id=cace9f1359874352, https://usegalaxy.org/published/workflow?id=d2c408df40dc311b, https://usegalaxy.org/published/workflow?id=ddf7a594b9609d68, https://usegalaxy.org/published/workflow?id=e887adf3afc3253d, https://usegalaxy.org/published/workflow?id=ea206593698adbfd, https://usegalaxy.org/published/workflow?id=fc2b48600853f3ea, https://workflowhub.eu/workflows/1594?version=1, https://workflowhub.eu/workflows/645?version=14 assembly/assembly-decontamination
pathview pathview Pathview is a tool set for pathway based data integration and visualization. 2019-08-26 https://bioconductor.org/packages/release/bioc/html/pathview.html 1.34.0 bioconductor-pathview 1.46.0 To update Statistics, RNA, Micro-array Analysis Pathway or network analysis, Pathway or network visualisation Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1546 1688 8322 9128 1410 1484 7998 8673 244 244 1526 1526 21 22 258 275 19602 18104 3438 3221 https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://workflowhub.eu/workflows/1713?version=1 transcriptomics/ref-based
pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference 2022-03-10 https://github.com/PacificBiosciences/gcpp 2.0.2 pbgcpp 2.0.2 Up-to-date Variant Analysis Variant calling Variant calling Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. 2022-03-10 https://github.com/PacificBiosciences/pbmm2 1.17.0 pbmm2 1.17.0 Up-to-date Next Gen Mappers Pairwise sequence alignment, Sorting Pairwise sequence alignment, Sorting Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 tree/master/tools/pbmm2" https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 41 229 229 0 0 0 0 0 0 0 0 0 0 0 0 229 229 41 41
pcdl pcdl_get_anndata, pcdl_get_cell_attribute, pcdl_get_cell_attribute_list, pcdl_get_cell_df, pcdl_get_celltype_list, pcdl_get_conc_attribute, pcdl_get_conc_df, pcdl_get_substrate_list, pcdl_get_unit_dict, pcdl_get_version, pcdl_make_cell_vtk, pcdl_make_conc_vtk, pcdl_make_gif, pcdl_make_graph_gml, pcdl_make_movie, pcdl_plot_contour, pcdl_plot_scatter, pcdl_plot_timeseries pcdl PhysiCell Data Loader. 2025-06-06 https://github.com/elmbeech/physicelldataloader 3.0.1+galaxy0 To update Systems Biology, Data Export, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl 0 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pdfimages pdfimages PDF image extractor. 2025-07-31 https://gitlab.freedesktop.org/poppler/poppler/ 25.07.0 poppler To update Imaging, Natural Language Processing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 15 15 0 0 0 0 0 0 0 0 0 0 0 0 15 15 2 2
pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. 2016-06-16 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram 1.0.2 openjdk To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 709 709 8778 8778 1037 1176 10416 11753 168 168 1076 1076 72 72 195 195 21802 20465 2125 1986 https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=25aa944237d7fb82, https://usegalaxy.eu/published/workflow?id=2f51a82838722bec, https://usegalaxy.eu/published/workflow?id=30e7dc81e323cbdb, https://usegalaxy.eu/published/workflow?id=3b8ef7905c902b27, 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peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. 2024-02-25 https://github.com/steinmann/peakzilla 1.0 python To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 73 73 0 0 0 0 0 0 0 0 0 0 0 0 73 73 19 19
pear iuc_pear PEAR evaluates all possible paired-end read overlaps 2015-02-11 https://cme.h-its.org/exelixis/web/software/pear/ 0.9.6 pear 0.9.6 Up-to-date Fastq Manipulation Sequence merging Sequence merging Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 416 448 9796 10458 665 1869 8692 23290 202 335 4780 8865 0 0 0 0 42613 23268 2652 1283 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://workflowhub.eu/workflows/232?version=1
pgxrpi pgx_freqplot, pgx_loader pgxLoader and pgxFreqplot functions from pgxRpi 2025-02-27 https://github.com/progenetix/pgxRpi 1.2.0 bioconductor-pgxrpi 1.2.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pgxRpi https://github.com/galaxyproject/tools-iuc/tree/main/tools/pgxRpi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes 2023-02-14 https://github.com/gbouras13/pharokka 1.3.2 \n pharokka\n To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 766 766 16933 16933 1 1 21 21 117 117 1202 1202 0 0 0 0 18156 18156 884 884
phyloseq phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.50.0 bioconductor-phyloseq 1.50.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. 4 1 7 6 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 251 251 3161 3161 156 156 1022 1022 35 35 190 190 14 14 163 163 4536 4536 456 456 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://workflowhub.eu/workflows/1395?version=2 microbiome/dada-16S
phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ 3.3.20220408 phyml 3.3.20220408 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 286 335 2452 2654 0 0 0 0 215 240 1475 1564 79 79 334 334 4552 4261 654 580 https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0
picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. 2017-01-11 http://broadinstitute.github.io/picard/ 3.1.1 picard 3.4.0 To update SAM Formatting Formatting Sequencing Sequencing devteam 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https://workflowhub.eu/workflows/1096?version=2, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1256?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1327?version=6, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1873?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/1882?version=2, https://workflowhub.eu/workflows/612?version=25, https://workflowhub.eu/workflows/625?version=27, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/694?version=8 statistics/flexynesis_classification
picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 44 63 562 1142 0 0 0 0 38 41 2348 2626 20 20 442 442 4210 3352 124 102
picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2021-07-09 https://github.com/picrust/picrust2/wiki 2.5.3 picrust2 2.6.2 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 327 327 6432 6432 1 1 1 1 64 64 2888 2888 0 0 0 0 9321 9321 392 392 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34
pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria 2016-08-11 https://github.com/broadinstitute/pilon/wiki 1.20.1 pilon 1.24 To update Variant Analysis Sequence assembly, Analysis, Read alignment Sequence assembly, Analysis Assembly Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1417 1484 10881 12166 1340 1411 8461 9526 985 1018 5002 5466 25 25 126 126 27284 24470 3938 3767 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=3588c40cab9b4e1d, https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://workflowhub.eu/workflows/1617?version=1 assembly/chloroplast-assembly
pimento pimento_are_there_primers, pimento_auto, pimento_choose_primer_cutoff, pimento_find_cutoffs, pimento_gen_bcv, pimento_std A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. 2025-08-04 https://github.com/EBI-Metagenomics/PIMENTO 1.0.2 mi-pimento 1.0.2 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1
pipelign pipelign Multipe sequence alignment 2019-08-20 https://github.com/asmmhossain/pipelign/ 0.2 pipelign 0.2 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 313 329 1909 1972 715 796 9356 9994 0 0 0 0 0 0 0 0 11966 11265 1125 1028
pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. 2017-09-03 https://github.com/pmelsted/pizzly/ 0.37.3.1 pizzly 0.37.3 To update Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25 30 2337 2381 71 89 2125 2362 0 0 0 0 0 0 0 0 4743 4462 119 96
plasclass plasclass PlasClass is a tool to classify sequences of plasmid or chromosomal origin 2025-07-31 https://github.com/Shamir-Lab/PlasClass 0.1.1 plasclass 0.1.1 Up-to-date Sequence Analysis Sequence classification, Sequence assembly, k-mer counting Sequence classification, Sequence assembly, k-mer counting Metagenomics, Sequence assembly, DNA, Metagenomic sequencing Metagenomics, Sequence assembly, DNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass PlasClass PlasClass PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow 1.1.0 plasflow 1.1.0 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 876 1004 55069 56639 757 797 7929 8195 87 87 3496 3496 0 0 0 0 68330 66494 1888 1720 https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore
plasmidfinder plasmidfinder "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1015 1015 35994 35994 623 623 11939 11939 211 211 3278 3278 48 48 10730 10730 61941 61941 1897 1897 https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/bacterial-genome-annotation
plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 2020-09-14 https://www.cog-genomics.org/plink 1.90b6.21 plink 1.90b6.21 Up-to-date Genome-Wide Association Study Genetic variation analysis Genetic variation analysis GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 191 191 1210 1210 105 105 1251 1251 0 0 0 0 7 7 67 67 2528 2528 303 303
polypolish polypolish "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." 2022-09-22 https://github.com/rrwick/Polypolish 0.6.1 polypolish 0.6.1 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 147 147 1066 1066 0 0 0 0 26 26 615 615 10 10 79 79 1760 1760 183 183 https://workflowhub.eu/workflows/1613?version=1 assembly/mrsa-nanopore
porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads 2018-09-13 https://github.com/rrwick/Porechop porechop 0.2.4 To update Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3888 4063 445549 452222 3090 3144 150171 150874 1362 1432 46371 65797 9 9 10935 10935 679828 653026 8648 8349 https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4a39d38fde81e35d, https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=4c7e0703aace6aa3, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=21161075002d6778, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=5626a440a5798458, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a, https://usegalaxy.org/published/workflow?id=b7817a12dbee583c, https://usegalaxy.org/published/workflow?id=badd4b56dbdeaba7, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/1439?version=1, https://workflowhub.eu/workflows/1473?version=1, https://workflowhub.eu/workflows/1492?version=2 assembly/mrsa-nanopore, microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data
poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 2017-12-17 https://poretools.readthedocs.io/en/latest/ 0.6.1a1 poretools 0.6.1a1 Up-to-date Fasta Manipulation, Fastq Manipulation Nucleic acid sequence analysis Nucleic acid sequence analysis DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 13 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 0 172 274 15702 21152 392 508 31358 42781 125 130 9684 11349 0 0 0 0 75282 56744 912 689
ppanggolin ppanggolin_all, ppanggolin_msa, ppanggolin_projection, ppanggolin_rarefaction Microbial Partitioned PanGenome 2025-01-22 https://github.com/labgem/PPanGGOLiN 2.2.5 ppanggolin 2.2.5 Up-to-date Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin ppanggolin PPanGGOLiN PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 55 249 249 0 0 0 0 0 0 0 0 16 16 67 67 316 316 71 71 genome-annotation/bacterial-pangenomics
presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. 2017-08-30 https://presto.readthedocs.io/ 0.6.2 presto 0.7.6 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequencing, DNA, Immunology Sequencing, DNA, Immunology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 331 401 75739 81623 0 0 0 0 0 0 0 0 81623 75739 401 331 https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a, https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa
prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 2016-05-30 http://prinseq.sourceforge.net/manual.html @TOOL_VERSION+galaxy2 prinseq 0.20.4 To update Fastq Manipulation, Metagenomics Read pre-processing, Sequence trimming, Sequence contamination filtering Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics Transcriptomics, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 345 412 15643 16651 1317 1501 10523 12474 0 0 0 0 11 11 17 17 29142 26183 1924 1673 https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1 microbiome/mgnify-amplicon
prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal 2.6.3 prodigal 2.6.3 Up-to-date Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 0 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 611 611 6456 6456 0 0 0 0 70 70 1515 1515 19 19 1487 1487 9458 9458 700 700 https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://workflowhub.eu/workflows/1663?version=1 ecology/marine_omics_bgc
progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner 2015-05-15 http://darlinglab.org/mauve/user-guide/progressivemauve.html progressivemauve snapshot_2015_02_13 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 788 861 2637 3053 1096 1189 3329 3750 0 0 0 0 1 1 1 1 6804 5967 2051 1885
prokka prokka Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka 1.14.6 prokka 1.14.6 Up-to-date Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, Model organisms, Virology crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 10459 11098 819587 847581 14547 16587 462648 506432 5094 6142 199279 229418 422 424 7463 7481 1590912 1488977 34251 30522 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=12653a1e65a20304, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, 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prot_scriber prot_scriber Protein annotation of short human readable descriptions 2022-05-10 https://github.com/usadellab/prot-scriber 0.1.6 prot-scriber 0.1.6 Up-to-date Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 9 9
proteinortho proteinortho, proteinortho_clustering, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. 2020-02-05 https://gitlab.com/paulklemm_PHD/proteinortho 6.3.6 proteinortho 6.3.6 Up-to-date Proteomics Sequence clustering, Sequence analysis Sequence clustering, Sequence analysis Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 432 463 5028 5485 0 0 0 0 0 0 0 0 4 4 23 23 5508 5051 467 436 https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep
psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. 2023-09-06 https://github.com/splicebox/PsiCLASS 1.0.3 psiclass 1.0.3 Up-to-date Transcriptomics Transcriptome assembly Transcriptome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 46 46 0 0 0 0 0 0 0 0 0 0 0 0 46 46 11 11
pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data 2018-04-26 https://github.com/skrakau/PureCLIP 1.0.4 pureclip 1.3.1 To update Sequence Analysis, RNA, CLIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 84 105 1337 1705 0 0 0 0 0 0 0 0 0 0 0 0 1705 1337 105 84 https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=8fb156020285e049
purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth 2021-02-03 https://github.com/dfguan/purge_dups 1.2.6 purge_dups 1.2.6 Up-to-date Assembly Genome assembly, Read binning, Scaffolding Genome assembly, Read binning, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. 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pycoqc pycoqc QC metrics for ONT Basecalling 2021-03-02 https://github.com/tleonardi/pycoQC 2.5.2 pycoqc 2.5.2 Up-to-date Nanopore Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Sequence analysis, Data quality management, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 832 832 23549 23549 1182 1182 4440 4440 606 606 1143 1143 158 158 322 322 29454 29454 2778 2778 https://usegalaxy.org.au/published/workflow?id=01393562b82f1884, https://usegalaxy.org.au/published/workflow?id=0d1d4392c3042fbd, https://usegalaxy.org.au/published/workflow?id=31dbe7344d72b903, https://usegalaxy.org.au/published/workflow?id=364025bd13970867, https://usegalaxy.org.au/published/workflow?id=419e09e4a2fa6d38, https://usegalaxy.org.au/published/workflow?id=5f4e164c18810cca, https://usegalaxy.org.au/published/workflow?id=866b69c5ee6601fe, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=98f285d6f0253b81, https://usegalaxy.org.au/published/workflow?id=c87b645aedfb857d, https://usegalaxy.org.au/published/workflow?id=da3d4b39b0d655e7, https://usegalaxy.org.au/published/workflow?id=ed43af416c6a7d3b, https://usegalaxy.org.au/published/workflow?id=fdf32312e8567093 sequence-analysis/quality-control
pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. 2018-06-08 https://github.com/deeptools/pyGenomeTracks 3.9 pygenometracks 3.9 Up-to-date Visualization Visualisation, Formatting Visualisation, Formatting Model organisms, Imaging, Workflows Model organisms, Imaging, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1301 1446 13377 16146 1427 1472 11997 12438 210 210 5014 5054 44 44 81 81 33719 30469 3172 2982 https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.org.au/published/workflow?id=13ce18408ee7acc9, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1568?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/1847?version=1, https://workflowhub.eu/workflows/420?version=3 epigenetics/atac-seq, epigenetics/hicexplorer, transcriptomics/differential-isoform-expression, transcriptomics/ref-based
pysradb_search pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. 2022-11-10 https://github.com/saketkc/pysradb 1.4.2 pysradb 2.4.1 To update Sequence Analysis Deposition, Data retrieval Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics Sequencing, Gene transcripts, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 178 178 0 0 0 0 0 0 0 0 0 0 0 0 178 178 44 44
qfilt qfilt Filter sequencing data 2018-06-06 https://github.com/veg/qfilt 1.0.0+galaxy1 qfilt 0.0.1 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qiime qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 183 242 2193 2749 0 0 0 0 1 1 2 2 9 9 18 18 2769 2213 252 193 https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4
qiime qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 32 32 0 0 0 0 0 0 0 0 0 0 32 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 418 483 34279 42817 1 1 1617 1617 1 1 2 16 17 17 4517 4550 49000 40415 502 437 https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 sequence-analysis/Manage_AB1_Sanger
qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts 2022-10-06 http://www.qiime.org 0.1.0 unzip To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 277 277 0 0 0 0 9 9 186 186 0 0 0 0 463 463 40 40 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34
qq_tools qq_manhattan 2020-10-07 https://CRAN.R-project.org/package=qqman 0.1.0 r-qqman 0.1.4 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 35 35 35 35 1 1 https://usegalaxy.fr/published/workflow?id=4ec0bc782472fa10
qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. 2019-10-10 http://qualimap.bioinfo.cipf.es/ 2.3 qualimap 2.3 Up-to-date Sequence Analysis, Transcriptomics, SAM Sequencing quality control Sequencing quality control Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 0 0 0 1 0 0 0 0 0 0 4 4 4 0 2949 3172 735774 740034 3586 3810 117198 120922 847 882 36259 41650 70 70 6924 6924 909530 896155 7934 7452 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quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. 2016-09-07 http://quast.bioinf.spbau.ru/ 5.3.0 quast 5.3.0 Up-to-date Assembly Visualisation, Sequence assembly validation Visualisation, Sequence assembly validation Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast quast QUAST QUAST stands for QUality ASsessment Tool. 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query_impc query_impc Contains a tool to query the IMPC database. 2023-10-11 https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc 0.9.0 requests To update Convert Formats, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 4 0 0 0 0 0 0 0 0 0 0 0 0 4 4 2 2
query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output 2017-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3 3 3 1 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 869 887 150015 159379 898 898 14092 14092 149 149 7881 7895 5 6 96 98 181464 172084 1940 1921 https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, 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ecology/Ecoregionalization_tutorial, galaxy-interface/ncbi-sarf, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/metagenomics-assembly, microbiome/mgnify-amplicon, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/neoantigen-fragpipe-discovery, proteomics/neoantigen-fusion-database-generation, proteomics/neoantigen-hla-binding-novel-peptides, proteomics/neoantigen-non-reference-database-generation, proteomics/neoantigen-peptide-verification, proteomics/neoantigen-predicting-hla-binding, proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-dbcreation, proteomics/proteogenomics-dbsearch, proteomics/proteogenomics-novel-peptide-analysis, transcriptomics/rna-interactome
quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity 2022-07-08 https://github.com/mahulchak/quickmerge 0.3 quickmerge 0.3 Up-to-date Assembly Genome assembly, Scaffolding, De-novo assembly, Genotyping Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
quicktree quicktree neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree 2.5 quicktree 2.5 Up-to-date Phylogenetics Phylogenetic inference (from molecular sequences) Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree quicktree QuickTree QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 69 69 466 466 0 0 0 0 0 0 0 0 0 0 0 0 466 466 69 69 https://workflowhub.eu/workflows/1650?version=1 sequence-analysis/tapscan-streptophyte-algae
raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis 2018-03-03 https://github.com/dgrun/RaceID3_StemID2_package/ 0.2.3 r-raceid 0.1.3 To update Single Cell, Transcriptomics Expression profile clustering, Expression analysis, Molecular dynamics Expression profile clustering, Expression analysis, Molecular dynamics Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid RaceID RaceID Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data 5 5 5 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 85 164 973 4613 433 438 3133 3209 4 5 2567 2969 1 1 1 1 10792 6674 608 523 https://usegalaxy.eu/published/workflow?id=2f8d9fb85242eca7, https://usegalaxy.org.au/published/workflow?id=9dfa217eae285c30, https://workflowhub.eu/workflows/1547?version=1 single-cell/scrna-raceid
ragtag ragtag Reference-guided scaffolding of draft genomes tool. 2021-11-10 https://github.com/malonge/RagTag 2.1.0 ragtag 2.1.0 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 774 774 8106 8106 6 6 59 59 108 108 2145 2145 32 32 416 416 10726 10726 920 920 https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489
rapidnj rapidnj Galaxy wrapper for the RapidNJ tool 2020-05-11 https://birc.au.dk/software/rapidnj/ 2.3.2 rapidnj 2.3.2 Up-to-date Phylogenetics Phylogenetic tree generation Phylogeny Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 57 57 3022 3022 285 303 1941 2185 31 31 291 291 13 13 44 44 5542 5298 404 386 https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://workflowhub.eu/workflows/1518?version=1 genome-annotation/gene-centric
rasusa rasusa Randomly subsample sequencing reads to a specified coverage 2024-02-16 https://github.com/mbhall88/rasusa 2.0.0 rasusa 2.2.2 To update Sequence Analysis Sequence assembly validation, Sequencing quality control Sequence assembly validation Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq Genomics, Sequence analysis, Sequence assembly, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa rasusa rasusa Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 24 104 104 0 0 0 0 0 0 0 0 0 0 0 0 104 104 24 24
raven raven Raven is a de novo genome assembler for long uncorrected reads. 2020-11-04 https://github.com/lbcb-sci/raven 1.8.3 raven-assembler 1.8.3 Up-to-date Assembly De-novo assembly, Genome assembly, Read pre-processing De-novo assembly, Genome assembly, Read pre-processing Sequence assembly, Whole genome sequencing, Genomics Sequence assembly, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven raven Raven a de novo genome assembler for long reads.Raven is a de novo genome assembler for long uncorrected reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 610 610 15837 15837 0 0 0 0 276 276 13041 13041 24 24 217 217 29095 29095 910 910
raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ 8.2.12 raxml 8.2.13 To update Phylogenetics Sequence analysis, Phylogenetic tree analysis Sequence analysis Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1422 1464 15492 16986 1144 1144 19599 19633 731 1034 5870 7945 21 21 305 305 44869 41266 3663 3318 https://usegalaxy.eu/published/workflow?id=470656ef317c9dd5, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1577?version=1 evolution/mtb_phylogeny
rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. 2018-05-02 https://github.com/mourisl/Rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 To update Fastq Manipulation Sequencing error detection Sequencing error detection RNA, RNA-Seq, Sequencing RNA, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 78 803 803 0 0 0 0 0 0 0 0 0 0 0 0 803 803 78 78
read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 3781 3781 8 8 9 9 0 0 0 0 0 0 0 0 3790 3790 89 89 https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1
recentrifuge recentrifuge "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." 2022-05-04 https://github.com/khyox/recentrifuge 1.16.1 recentrifuge 1.16.1 Up-to-date Metagenomics Taxonomic classification, Expression analysis, Cross-assembly Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 306 306 2546 2546 160 160 593 593 37 37 105 105 27 27 2397 2397 5641 5641 530 530 https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=c14d2e8b3c191bc4, https://usegalaxy.eu/published/workflow?id=c930a54a30dcc7e3, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2a782ad24271f570, https://usegalaxy.org/published/workflow?id=323c651ca583c9e5, https://usegalaxy.org/published/workflow?id=4f698eaeef30e364, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=1, https://workflowhub.eu/workflows/1881?version=1, https://workflowhub.eu/workflows/1882?version=2 ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control
red red Red (REpeat Detector) 2022-09-14 https://github.com/BioinformaticsToolsmith/Red 2018.09.10 red 2018.09.10 Up-to-date Sequence Analysis RNA-Seq analysis, Editing RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation RNA, Sequencing, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 362 362 1237 1237 277 277 556 556 86 86 369 369 60 60 177 177 2339 2339 785 785 https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4a71a1e08a4a8e61, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://workflowhub.eu/workflows/1538?version=2, https://workflowhub.eu/workflows/753?version=1 genome-annotation/repeatmasker
regex_switch regex_switch Regex switch 2025-10-09 https://github.com/galaxyproject/tools-iuc/tree/main/tools/regex_switch 1.0.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/regex_switch https://github.com/galaxyproject/tools-iuc/tree/main/tools/regex_switch 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2018-04-21 http://www.repeatmasker.org/ 4.1.5 repeatmasker 4.2.1 To update Sequence Analysis Genome annotation Genome annotation Sequence analysis, Sequence composition, complexity and repeats Sequence composition, complexity and repeats bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1428 1448 10157 10293 1181 1219 9955 10202 413 413 4594 4594 91 91 610 610 25699 25316 3171 3113 https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=4a71a1e08a4a8e61, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050, https://usegalaxy.org/published/workflow?id=fb8b997f516288e1, https://workflowhub.eu/workflows/1538?version=2, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/753?version=1, https://workflowhub.eu/workflows/875?version=3 ecology/phylogeny-data-prep, genome-annotation/repeatmasker
repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA 2021-08-26 https://www.repeatmasker.org/RepeatModeler/ 2.0.5 To update Genome annotation Repeat sequence detection Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats Sequence composition, complexity and repeats, Sequence composition, complexity and repeats csbl https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 725 725 9423 9423 424 424 2473 2473 240 240 8995 8995 30 30 270 270 21161 21161 1419 1419 https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/875?version=3 genome-annotation/repeatmasker
repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. 2015-12-18 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 224 254 727 0 0 0 0 0 0 0 0 727 254 224 96
reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast 2017-05-26 https://cran.r-project.org/web/packages/reshape2/index.html 1.4.2 r-reshape2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 112 123 3506 3687 100 131 421 585 0 0 0 0 3 3 6 6 4278 3933 257 215 https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://workflowhub.eu/workflows/1189?version=2
resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. 2016-01-13 1.0.2 python To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 9 13 86 22 60 36 221 0 0 0 0 0 0 0 0 307 49 69 28 https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11
revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers 2024-03-19 https://gitlab.com/Bernt/revoluzer/ 0.1.8 revoluzer 0.1.8 Up-to-date Phylogenetics Structural variation detection Structural variation detection Molecular evolution, Phylogeny Molecular evolution, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 68 68 3932 3932 0 0 0 0 0 0 0 0 0 0 0 0 3932 3932 68 68
rgcca rgcca multi-block analysis 2020-09-02 https://github.com/rgcca-factory/RGCCA 3.0.2 rgccacmd 3.0.3 To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 46 46 40 40 94 94 0 0 0 0 0 0 0 0 140 140 47 47
rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper 2015-05-18 https://github.com/alexdobin/STAR 2.7.11b star 2.7.11b Up-to-date Next Gen Mappers, Transcriptomics, Single Cell Sequence alignment Sequence alignment RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar star STAR Ultrafast universal RNA-seq data aligner 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 11597 13300 454740 555235 17153 22174 406678 513360 1461 1710 55618 62678 1016 1019 12202 12241 1143514 929238 38203 31227 https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=06fe33c4420906bf, https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, 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ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data 2022-09-22 https://github.com/LabTranslationalArchitectomics/riboWaltz 1.2.0 ribowaltz 2.0 To update Transcriptomics, RNA Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 21 21 204 204 0 0 0 0 0 0 0 0 0 0 0 0 204 204 21 21
rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. 2020-10-05 https://github.com/ablab/rnaquast 2.3.0 rnaquast 2.3.0 Up-to-date Assembly, RNA De-novo assembly, Transcriptome assembly, Sequence assembly validation De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-Seq Sequence assembly, Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 375 375 1887 1887 196 196 767 767 31 31 326 326 11 11 103 103 3083 3083 613 613 https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://workflowhub.eu/workflows/1688?version=1 transcriptomics/differential-isoform-expression
roary roary Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ 3.13.0 roary 3.13.0 Up-to-date Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2251 2377 21218 23887 2319 2454 17744 18851 653 749 5251 7169 47 47 187 187 50094 44400 5627 5270 https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a
rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output 2023-01-05 https://github.com/brsynth/rp2biosensor 3.2.1 rp2biosensor To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 2022-10-17 https://github.com/brsynth/rp2paths 2.0.0 rp2paths To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1581?version=1 synthetic-biology/retrosynthesis_analysis
rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files 2022-03-30 https://github.com/brsynth/rpbasicdesign 1.2.2 rpbasicdesign To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1576?version=1 synthetic-biology/basic_assembly_analysis
rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways 2022-01-17 https://github.com/brsynth/rptools/releases 5.12.3 rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1572?version=1 synthetic-biology/pathway_analysis
rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format 2022-11-16 https://github.com/brsynth/rptools 5.13.1 rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rrmscorer rrmscorer Predicts RNA Recognition Motif (RRM) scores for protein sequences. 2025-09-17 https://bio2byte.be/rrmscorer/ 1.0.11 rrmscorer 1.0.11 Up-to-date Sequence Analysis Multiple sequence alignment, Calculation, Visualisation Multiple sequence alignment, Calculation, Visualisation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer RRMScorer RRMScorer RRMScorer provides quick predictions for any RNA recognition motif (RRM) and any RNA target purely based on their sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rrparser rrparser Reaction Rules Parser 2022-06-27 https://github.com/brsynth/RRParser 2.7.0 rrparser To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1581?version=1 synthetic-biology/retrosynthesis_analysis
rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. 22 22 22 22 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 22 0 0 0 0 0 0 22 22 22 0 4113 5223 155237 181534 4079 5016 146353 197501 629 697 28108 32069 809 810 78294 78366 489470 407992 11746 9630 https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=5d83e0886f2a7465, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.fr/published/workflow?id=826cffb2458e4067, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=af7b95f46485308c, https://usegalaxy.org.au/published/workflow?id=b08342866a118a5e, https://usegalaxy.org.au/published/workflow?id=bb0feff5d764df60, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=73f5b1a6fd3c703f, https://usegalaxy.org/published/workflow?id=76b8ed1c68678b62, https://usegalaxy.org/published/workflow?id=7e9269e78e989480, https://usegalaxy.org/published/workflow?id=a743746151101352, https://usegalaxy.org/published/workflow?id=b11796364c22235e, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1675?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1692?version=1, https://workflowhub.eu/workflows/1695?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/688?version=1 transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts
ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data 2018-08-30 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 1.26.0 bioconductor-ruvseq 1.40.0 To update Transcriptomics, RNA, Statistics Differential gene expression analysis Differential gene expression analysis Gene expression, RNA-seq Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 155 200 1182 1507 272 319 2100 2428 0 0 0 0 0 0 0 0 3935 3282 519 427
salsa salsa A tool to scaffold long read assemblies with Hi-C 2021-01-14 https://github.com/marbl/SALSA 2.3 salsa2 2.3 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Sequence assembly, DNA binding sites, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 130 130 495 495 103 103 1074 1074 24 24 410 410 0 0 0 0 1979 1979 257 257 https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://workflowhub.eu/workflows/1607?version=1 assembly/vgp_genome_assembly
samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files 2016-12-18 https://github.com/GregoryFaust/samblaster 0.1.26 samblaster 0.1.26 Up-to-date SAM, Fastq Manipulation, Variant Analysis Split read mapping Split read mapping DNA, Sequencing, Mapping DNA, Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
samtools 2017-01-24 https://github.com/samtools/samtools 1.22 samtools 1.22.1 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sansa sansa_annotate Sansa is a tool for structural variant annotation. 2020-12-05 https://github.com/dellytools/sansa 0.2.2 sansa 0.2.5 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 43 43 157 157 0 0 0 0 0 0 0 0 0 0 0 0 157 157 43 43
sarscov2formatter sarscov2formatter sarscov2formatter custom script 2020-05-01 https://github.com/nickeener/sarscov2formatter 1.0 sarscov2formatter 1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14 16 40 174 26 30 48 402 0 0 0 0 0 0 0 0 576 88 46 40 https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
sarscov2summary sarscov2summary sarscov2summary custom script 2020-05-01 https://github.com/nickeener/sarscov2summary 0.1 sarscov2summary 0.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 5 3 140 3 6 4 253 0 0 0 0 0 0 0 0 393 7 11 6 https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e
sbml2sbol sbml2sbol Convert SBML to SBOL format 2022-10-15 https://github.com/neilswainston/SbmlToSbol 0.1.13 sbml2sbol To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python 2019-03-04 https://scanpy.readthedocs.io 1.10.2 scanpy 1.7.2 To update Single Cell, Spatial Omics, Transcriptomics Differential gene expression analysis, Principal component visualisation, Expression profile clustering Differential gene expression analysis, Principal component visualisation, Expression profile clustering Gene expression, Cell biology, Genetics, Single-cell sequencing Gene expression, Cell biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 771 868 70187 77433 456 465 42066 42163 120 121 22195 23258 2 2 114 114 142968 134562 1456 1349 https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=21315ffd2df2f159, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=4756053b2596b6cf, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=77e85bde57477194, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=921cab3e6faf30be, https://usegalaxy.eu/published/workflow?id=9adf0402b641042c, https://usegalaxy.eu/published/workflow?id=9d15b328d8408715, https://usegalaxy.eu/published/workflow?id=ae79275d3568ad31, https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d70dc4cfeedb690b, https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514, https://usegalaxy.eu/published/workflow?id=ddced7b107e4707a, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e472096116cbe392, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.org.au/published/workflow?id=102eb726f63f3190, https://usegalaxy.org.au/published/workflow?id=106080375ad4eaaa, https://usegalaxy.org.au/published/workflow?id=218ffb4438833bdd, https://usegalaxy.org.au/published/workflow?id=57321b64220d5835, https://usegalaxy.org.au/published/workflow?id=8055596d732590d6, https://usegalaxy.org.au/published/workflow?id=8bc01c1fdd62ad12, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://usegalaxy.org/published/workflow?id=ea3257e0ef9f505a, https://usegalaxy.org/published/workflow?id=f35ccb693cd874c1, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1256?version=1, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1362?version=1, https://workflowhub.eu/workflows/1485?version=1, https://workflowhub.eu/workflows/1490?version=1, https://workflowhub.eu/workflows/1496?version=1, https://workflowhub.eu/workflows/1501?version=1, https://workflowhub.eu/workflows/1502?version=1, https://workflowhub.eu/workflows/1519?version=1, https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1556?version=1, https://workflowhub.eu/workflows/1574?version=1, https://workflowhub.eu/workflows/467?version=4, https://workflowhub.eu/workflows/468?version=3 single-cell/pseudobulk-analysis, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-plant, single-cell/scrna-scanpy-pbmc3k
scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. 2019-07-18 http://bioconductor.org/packages/scater/ 1.22.0 bioconductor-scater 1.34.1 To update Single Cell, Transcriptomics, Visualization Read pre-processing, Sequencing quality control, Sequence visualisation Read pre-processing, Sequence visualisation RNA-Seq, Quality affairs, Molecular genetics RNA-Seq, Quality affairs, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 77 94 1007 1409 0 0 0 0 7 8 1094 1215 0 0 0 0 2624 2101 102 84 https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8, https://usegalaxy.org.au/published/workflow?id=3c9140288202aa76, https://workflowhub.eu/workflows/1511?version=1 single-cell/scrna-scater-qc
sceasy_convert sceasy_convert Converter between difference single-cell formats 2023-11-10 https://github.com/cellgeni/sceasy/ 0.0.7 r-sceasy 0.0.7 Up-to-date Single Cell, Spatial Omics, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy sceasy sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 301 310 1543 1615 103 104 521 522 5 5 349 349 1 1 2 2 2488 2415 420 410 https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 single-cell/EBI-retrieval, single-cell/scrna-case_alevin, single-cell/scrna-data-ingest
schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. 2019-12-16 https://github.com/joachimwolff/schicexplorer 4 schicexplorer 7 To update Sequence Analysis, Transcriptomics, Visualization, Single Cell Validation, Visualisation, Standardisation and normalisation Validation, Visualisation, Standardisation and normalisation Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer hicexplorer HiCExplorer A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.HiCExplorer — HiCExplorer 3.6 documentation.scHiCExplorer — scHiCExplorer 7 documentation.Free document hosting provided by Read the Docs. 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 8 11 99 821 12 12 32 32 2 2 1351 1351 0 0 0 0 2204 1482 25 22
scikit_bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics 2016-05-31 http://scikit-bio.org/ 0.4.2 scikit-bio 0.4.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 303 445 1472 2106 0 0 0 0 0 0 0 0 2107 1473 446 304 https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927
scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary 1.6.16 scoary 1.6.16 Up-to-date Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 113 113 1366 1366 0 0 0 0 0 0 0 0 0 0 0 0 1366 1366 113 113
scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data 2018-08-12 http://bioconductor.org/packages/release/bioc/html/scPipe.html 1.0.0+galaxy2 bioconductor-scpipe 2.6.0 To update Transcriptomics, Single Cell Genome annotation, Validation, Alignment, Visualisation Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing Gene expression, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 25 40 149 643 50 63 656 799 1 1 1 1 0 0 0 0 1443 806 104 76 https://usegalaxy.eu/published/workflow?id=0a692a2e643b9e1a
seaborn seaborn, seaborn_pairgrid Seaborn is a Python data visualization library based on Matplotlib. 2025-05-13 https://seaborn.pydata.org/ 0.13.2 seaborn To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. 2020-02-05 https://github.com/FredHutch/SEACR 1.3 seacr 1.3 Up-to-date Epigenetics, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 150 155 6871 7014 289 289 8117 8117 0 0 0 0 0 0 0 0 15131 14988 444 439 https://usegalaxy.eu/published/workflow?id=719314fa5263b501
selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. 2022-06-29 https://github.com/brsynth/selenzy-wrapper 0.3.0 selenzy_wrapper 0.3.0 Up-to-date Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.1.0 semibin 2.2.0 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. 1 6 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 53 53 2779 2779 9 9 18 18 0 0 0 0 2 2 75 75 2872 2872 64 64 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3
seq2hla seq2hla Precision HLA typing and expression from RNAseq data 2020-02-20 https://github.com/TRON-Bioinformatics/seq2HLA 2.3 seq2hla 2.3 Up-to-date Sequence Analysis Read mapping, Genetic variation analysis Read mapping, Genetic variation analysis Transcriptomics, Mapping Transcriptomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 65 432 482 11 11 49 49 6 6 102 102 0 0 0 0 633 583 82 79 https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.eu/published/workflow?id=db270d0eb035609e, https://usegalaxy.org.au/published/workflow?id=2249ab6710f5e84d, https://usegalaxy.org/published/workflow?id=1d925422fc6094a0, https://workflowhub.eu/workflows/1430?version=1, https://workflowhub.eu/workflows/1794?version=1 proteomics/neoantigen-predicting-hla-binding
seqcomplexity seqcomplexity Sequence complexity for raw reads 2022-06-07 https://github.com/stevenweaver/seqcomplexity 0.1.2 seqcomplexity 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 25 25 84 84 55 55 133 133 0 0 0 0 0 0 0 0 217 217 80 80
seqkit seqkit_fx2tab, seqkit_grep, seqkit_head, seqkit_locate, seqkit_sort, seqkit_split2, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.10.1 seqkit 2.10.1 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. 2 6 7 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 396 396 13926 13926 0 0 0 0 120 120 2190 2190 69 69 648 648 16764 16764 585 585 https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/697?version=1
seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. 2024-01-15 https://github.com/jstjohn/SeqPrep 1.3.2 seqprep 1.3.2 Up-to-date Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 227 3602 3602 0 0 0 0 0 0 0 0 0 0 0 0 3602 3602 227 227 microbiome/mgnify-amplicon
seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data 2023-11-07 https://github.com/denglab/SeqSero2 1.3.2 seqsero2 1.3.2 Up-to-date Sequence Analysis Genome indexing, Antimicrobial resistance prediction, Genome alignment Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Whole genome sequencing, Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 seqsero2 SeqSero2 rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 116 116 14011 14011 0 0 0 0 0 0 0 0 2 2 2 2 14013 14013 118 118 https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1
seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats 2015-01-13 https://github.com/lh3/seqtk 1.5 seqtk 1.5 Up-to-date Sequence Analysis Data handling, Sequence file editing Data handling, Sequence file editing Data management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. 15 15 15 15 0 0 0 0 0 0 0 0 0 0 15 0 14 0 0 0 0 0 15 0 0 0 0 0 0 15 15 14 0 804 862 270417 273634 956 1098 107899 122221 260 262 158312 159084 55 55 18691 18691 573630 555319 2277 2075 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=324c683a8e2fa5b0, https://usegalaxy.org.au/published/workflow?id=462beb964c99619d, https://usegalaxy.org.au/published/workflow?id=5cfea39918e8632d, https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=1ba0239e55ac0d07, https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a, https://usegalaxy.org/published/workflow?id=35c2626849348f2c, https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa, https://usegalaxy.org/published/workflow?id=62316da77b1bfa5a, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=7610b7797d71993a, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1327?version=6, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1629?version=1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1631?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1653?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1, https://workflowhub.eu/workflows/880?version=1 assembly/assembly-with-preprocessing, assembly/metagenomics-assembly, contributing/create-new-tutorial, microbiome/metagenomics-assembly, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/human-reads-removal, variant-analysis/aiv-analysis
sequali sequali Fast sequencing data quality metrics for short and long reads 2025-03-19 https://sequali.readthedocs.io/ 1.0.2 sequali 1.0.2 Up-to-date Fastq Manipulation Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Data quality management, Sequence analysis Data quality management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sequali https://github.com/galaxyproject/tools-iuc/tree/main/tools/sequali sequali Sequali Fast sequencing data quality metrics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 16 16 0 0 0 0 0 0 0 0 0 0 0 0 16 16 9 9
seqwish seqwish Alignment to variation graph inducer 2020-04-06 https://github.com/ekg/seqwish 0.7.5 seqwish 0.7.11 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 271 0 0 0 0 0 0 0 0 0 0 0 0 271 0 2 0 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40
seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics 2018-08-20 https://satijalab.org/seurat/ 5.0 r-seurat 3.0.2 To update Single Cell, Transcriptomics, Sequence Analysis RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat seurat Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 7 7 7 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 120 120 6468 6468 109 109 2871 2871 9 9 1332 1332 4 4 105 105 10776 10776 242 242 https://usegalaxy.eu/published/workflow?id=10c5d0560b977a6f, https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958, https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf, https://usegalaxy.org/published/workflow?id=59554bfcad77e307, https://workflowhub.eu/workflows/1555?version=1, https://workflowhub.eu/workflows/1560?version=1, https://workflowhub.eu/workflows/1570?version=1 single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-seurat-pbmc3k
sfold sfold Predict the probable RNA secondary structures through structure ensemble sampling 2024-10-09 https://github.com/Ding-RNA-Lab/Sfold 2.2.0 To update RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sfold https://github.com/galaxyproject/tools-iuc/tree/main/tools/sfold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2
shasta shasta Fast de novo assembly of long read sequencing data 2020-11-11 https://github.com/chanzuckerberg/shasta 0.6.0 shasta 0.14.0 To update Assembly, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 399 399 1291 1291 0 0 0 0 98 98 791 791 0 0 0 0 2082 2082 497 497
shorah_amplicon shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode 2018-11-27 https://github.com/cbg-ethz/shorah/blob/master/README.md 1.1.3 shorah 1.99.2 To update Sequence Analysis Haplotype mapping, Variant calling Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics Metagenomics, Sequencing, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
shovill shovill Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill 1.1.0 shovill 1.1.0 Up-to-date Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3269 3491 70801 76107 4933 5212 51724 55190 1425 1669 30312 35794 83 83 9136 9136 176227 161973 10455 9710 https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a727e22dc0431614, https://usegalaxy.eu/published/workflow?id=b5ffba506152b1a1, https://usegalaxy.eu/published/workflow?id=b90585626a793502, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=8ebc2b1ae24ed884, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=e75bd7d392e65209, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/103?version=1, https://workflowhub.eu/workflows/1043?version=11, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1602?version=1, https://workflowhub.eu/workflows/1767?version=1, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 assembly/mrsa-illumina
sickle sickle A windowed adaptive trimming tool for FASTQ files using quality 2015-11-03 https://github.com/najoshi/sickle 1.33.3 sickle-trim 1.33 To update Fastq Manipulation, Sequence Analysis Sequence trimming Sequence trimming Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 627 731 20571 21706 1315 1394 11397 12999 0 0 0 0 147 149 1215 1324 36029 33183 2274 2089 https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.org/published/workflow?id=fca70e1bf761c6a2
simpleweather simple_weather provides simple weather in text format 2016-07-19 http://wttr.in/ 0.1.2 curl To update Visualization, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. 2021-02-28 https://github.com/dlal-group/simtext 0.0.2 r-argparse 1.0.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 32 32 234 234 0 0 0 0 5 5 608 608 0 0 0 0 842 842 37 37 https://workflowhub.eu/workflows/1603?version=1 statistics/text-mining_simtext
sina sina SINA reference based multiple sequence alignment 2019-10-11 https://sina.readthedocs.io/en/latest/ 1.7.2 sina 1.7.2 Up-to-date Sequence Analysis Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 123 143 1180 1492 377 460 2041 2558 0 0 0 0 0 0 0 0 4050 3221 603 500
sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools 2023-04-12 https://github.com/timoast/sinto 0.10.1 sinto 0.10.1 Up-to-date Single Cell, Epigenetics Bioinformatics, Cell biology Bioinformatics, Cell biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto sinto sinto Sinto is a toolkit for processing aligned single-cell data. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 48 48 350 350 28 28 221 221 1 1 190 190 0 0 0 0 761 761 77 77 https://workflowhub.eu/workflows/1506?version=1 single-cell/scatac-preprocessing-tenx
slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads 2018-10-05 http://t-neumann.github.io/slamdunk 0.4.3 slamdunk 0.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10 13 159 402 55 57 1312 1380 0 0 0 0 0 0 0 0 1782 1471 70 65
sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. 2023-05-30 https://github.com/pachterlab/sleuth 0.30.2 r-sleuth 0.30.2 Up-to-date Transcriptomics, RNA, Statistics Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-Seq, Gene expression, Statistics and probability RNA-Seq, Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 42 42 204 204 0 0 0 0 0 0 0 0 0 0 0 0 204 204 42 42
smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. 2023-05-30 https://github.com/cbg-ethz/smallgenomeutilities 0.5.2 smallgenomeutilities 0.5.2 Up-to-date Sequence Analysis Read pre-processing, Sequence alignment, Genetic variation analysis Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Genomics, Population genetics, Workflows, Virology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 15 15 168 168 0 0 0 0 0 0 0 0 0 0 0 0 168 168 15 15
smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing 2022-06-30 https://github.com/KamilSJaron/smudgeplot 0.2.5 smudgeplot 0.4.0 To update Assembly Sequence trimming, Genotyping, k-mer counting Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Sequence assembly, Genetic variation, Mathematics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 146 146 805 805 90 90 242 242 78 78 1315 1315 0 0 0 0 2362 2362 314 314 https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/698?version=1 assembly/ERGA-post-assembly-QC
snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. 2017-10-12 https://github.com/KorfLab/SNAP 2013_11_29 snap 2013_11_29 Up-to-date Sequence Analysis Gene prediction Gene prediction DNA, DNA polymorphism, Genetics DNA polymorphism, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 348 410 1443 1821 258 292 813 939 100 101 578 594 0 0 0 0 3354 2834 803 706 https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://workflowhub.eu/workflows/1504?version=1 genome-annotation/annotation-with-maker
snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis 2024-05-16 https://kzhang.org/SnapATAC2/ 2.6.4 To update Single Cell, Epigenetics Essential dynamics, Dimensionality reduction, Gene expression profiling Essential dynamics, Dimensionality reduction, Gene expression profiling Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 snapatac SnapATAC SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 2521 2521 14 14 65 65 1 1 1633 1633 0 0 0 0 4219 4219 29 29 https://usegalaxy.eu/published/workflow?id=15cb6b690d23e6ef, https://usegalaxy.eu/published/workflow?id=d20fbb95f15386f5, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1089?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1561?version=1 single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-standard-processing-snapatac2
sniffles sniffles Galaxy wrapper for sniffles 2020-08-29 https://github.com/fritzsedlazeck/Sniffles 2.5.2 sniffles 2.6.3 To update Sequence Analysis Sequence analysis, Structural variation detection Sequence analysis, Structural variation detection DNA structural variation, Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 205 205 1813 1813 246 246 1546 1546 98 98 2716 2716 4 4 11 11 6086 6086 553 553 https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=35a9136ddf37d589, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399
snipit snipit Summarise snps relative to a reference sequence 2022-07-17 https://github.com/aineniamh/snipit 1.6 snipit 1.6 Up-to-date Variant Analysis, Sequence Analysis Base position variability plotting Base position variability plotting Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit snipit snipit Summarise snps relative to a reference sequence 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 88 88 1354 1354 16 16 84 84 0 0 0 0 0 0 0 0 1438 1438 104 104 https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://workflowhub.eu/workflows/1260?version=2
snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy snippy 4.6.0 To update Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3483 3838 188403 199916 4057 4306 138187 142349 2223 2852 67168 78979 60 60 8769 8769 430013 402527 11056 9823 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=464b642261ed7452, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=920aab45ff028ed4, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=d92f9c33dded693f, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=1719e0eb54b41f68, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=5674956f5c18b85b, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=ee4679b3e9e830b7, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1639?version=1, https://workflowhub.eu/workflows/1647?version=1 evolution/mtb_transmission, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis
snp_dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment 2019-10-18 https://github.com/tseemann/snp-dists 0.8.2 snp-dists 0.8.2 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1166 1178 9794 10000 353 353 8021 8021 282 282 2937 2937 0 0 0 0 20958 20752 1813 1801 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=d5cf994c03a60fa4, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1569?version=1 evolution/mtb_transmission
snp_sites snp_sites Finds SNP sites from a multi-FASTA alignment file 2017-06-28 https://github.com/sanger-pathogens/snp-sites 2.5.1 snp-sites 2.5.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 990 1009 10043 10330 466 466 3029 3029 166 168 3008 3022 0 0 0 0 16381 16080 1643 1622 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://workflowhub.eu/workflows/1569?version=1 evolution/mtb_transmission
snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox 2014-11-11 http://snpeff.sourceforge.net/ 5.2 biopython 1.70 To update Genome-Wide Association Study, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff 5 5 5 5 0 0 0 0 0 0 1 0 0 0 0 5 5 0 0 0 0 0 5 0 0 0 0 0 0 5 5 5 0 5886 6736 100316 146690 9237 14794 119649 216751 1196 1451 15667 18565 401 403 1954 4043 386049 237586 23384 16720 https://usegalaxy.eu/published/workflow?id=0882300f7b399587, https://usegalaxy.eu/published/workflow?id=112422839b68db02, https://usegalaxy.eu/published/workflow?id=1c5588d6ac7f773f, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2aede5c6577b28f5, https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, 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https://workflowhub.eu/workflows/1682?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/353?version=1, https://workflowhub.eu/workflows/357?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/363?version=2, https://workflowhub.eu/workflows/36?version=1 introduction/galaxy-intro-ngs-data-managment, variant-analysis/dip, variant-analysis/exome-seq, variant-analysis/mapping-by-sequencing, variant-analysis/somatic-variants, variant-analysis/trio-analysis
snpeff_sars_cov_2 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox 2020-06-17 http://snpeff.sourceforge.net/ To update Genome-Wide Association Study, Variant Analysis SNP detection SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs DNA polymorphism, Nucleic acid sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1580 1592 704888 766978 1876 1910 84580 99497 607 607 30784 32363 29 29 3465 3465 902303 823717 4138 4092 https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=03d1d2e0dc6e2024, https://usegalaxy.eu/published/workflow?id=0599f049e4697839, https://usegalaxy.eu/published/workflow?id=07b74e4cf53cb633, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=0e5b701ed5ca69a7, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=1761092d0e7deece, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=2a39dbc8fc6dd5d3, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, 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snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region 2020-12-02 https://github.com/BrownfieldPlantLab/SNPFreqPlot 1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 399 399 3862 3862 525 525 1655 1655 103 103 1386 1386 9 9 347 347 7250 7250 1036 1036 https://usegalaxy.eu/published/workflow?id=036990ecf300a99f, https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16, https://usegalaxy.eu/published/workflow?id=0c94260298199d8b, https://usegalaxy.eu/published/workflow?id=20592f292c205954, https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312, https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb, https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f, https://usegalaxy.eu/published/workflow?id=70ec8b1719e25982, https://usegalaxy.eu/published/workflow?id=88f5cef7e4146520, https://usegalaxy.eu/published/workflow?id=9eb29cc96d8d75c2, https://usegalaxy.eu/published/workflow?id=eb03839cc36048f5, https://usegalaxy.fr/published/workflow?id=798c8ff19825ab2c, https://usegalaxy.fr/published/workflow?id=b168a179d1b456cb, https://usegalaxy.org.au/published/workflow?id=1764bb1f506212e8, https://usegalaxy.org.au/published/workflow?id=1782d699b0166725, https://usegalaxy.org.au/published/workflow?id=5a975438c8752269, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=7cc2b5010c56f117, https://usegalaxy.org.au/published/workflow?id=800d28ec61b15244, https://usegalaxy.org.au/published/workflow?id=8e2b94c6fbf44368, https://usegalaxy.org.au/published/workflow?id=989eb73372135796, https://usegalaxy.org.au/published/workflow?id=b601f48ecec15bf4, https://usegalaxy.org.au/published/workflow?id=b920b02a23f94d11, https://usegalaxy.org.au/published/workflow?id=d0d6743450e5060d, https://usegalaxy.org.au/published/workflow?id=fbc732db2a2821b0, https://usegalaxy.org/published/workflow?id=07e761b2501971c6, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2b09f3c9465ee054, https://usegalaxy.org/published/workflow?id=2dceaa255cc8cf83, https://usegalaxy.org/published/workflow?id=6c2bb2209aad5e44, https://usegalaxy.org/published/workflow?id=7af656b8ea5e7e2e, https://usegalaxy.org/published/workflow?id=8a01c78688beae1d, https://usegalaxy.org/published/workflow?id=dcbc71347300822d, https://usegalaxy.org/published/workflow?id=f58c90061c31bd48, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://workflowhub.eu/workflows/109?version=9
snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html snpsift 5.3.0a To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift 8 8 8 8 0 0 0 0 0 0 8 0 0 0 0 0 8 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 2060 2117 5092180 5175645 3160 4102 368540 447226 502 515 105403 108005 39 40 11506 11523 5742399 5577629 6774 5761 https://usegalaxy.eu/published/workflow?id=036990ecf300a99f, https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16, https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=0c94260298199d8b, https://usegalaxy.eu/published/workflow?id=1c5588d6ac7f773f, https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=20592f292c205954, https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312, https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb, https://usegalaxy.eu/published/workflow?id=2f1ee01aeee2b9f0, https://usegalaxy.eu/published/workflow?id=35629b113a6f23ab, https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=40d2c7ac42bd5302, https://usegalaxy.eu/published/workflow?id=4a89ddab941c6819, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, 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https://workflowhub.eu/workflows/110?version=11, https://workflowhub.eu/workflows/1190?version=1, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/1391?version=1, https://workflowhub.eu/workflows/1479?version=1, https://workflowhub.eu/workflows/1540?version=1, https://workflowhub.eu/workflows/1642?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/354?version=1, https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 galaxy-interface/collections, galaxy-interface/workflow-automation, introduction/galaxy-intro-ngs-data-managment, microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/sars-cov-2
snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP snpsift 5.3.0a To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21 25 70 82 62 77 297 425 0 0 0 0 0 0 0 0 507 367 102 83 https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4
snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#geneSets snpsift 5.3.0a To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 105 149 570 644 179 218 437 534 0 0 0 0 0 0 0 0 1178 1007 367 284
socru socru Order and orientation of complete bacterial genomes 2019-09-03 https://github.com/quadram-institute-bioscience/socru 2.1.7 socru 2.2.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 41 52 571 679 90 107 278 320 0 0 0 0 0 0 0 0 999 849 159 131
sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2
spacexr spacexr_cside, spacexr_rctd Cell type identification and cell type-specific differential expression in spatial transcriptomics 2024-08-02 https://github.com/dmcable/spacexr/tree/master 2.2.1 r-spacexr 2.2.1 Up-to-date Spatial Omics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spacexr https://github.com/galaxyproject/tools-iuc/tree/main/tools/spacexr 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7 7 0 0 0 0 0 0 0 0 0 0 0 0 7 7 2 2
spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2016-12-21 https://github.com/ablab/spades 4.2.0 spades 4.2.0 Up-to-date Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 2 3 8 0 0 0 0 0 3 0 0 0 0 0 0 3 9 3 0 8250 8882 104429 116176 14023 14731 147425 154112 5211 6722 62902 76811 373 380 2677 2762 349861 317433 30715 27857 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a847773b563b2328, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=db10c092fad70d69, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=39c724282ee008e3, https://usegalaxy.org.au/published/workflow?id=813a4938397cf6ee, https://usegalaxy.org.au/published/workflow?id=87cdeb05b1ebeab0, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=15cca0e249f40aea, https://usegalaxy.org/published/workflow?id=18899840e49d89c3, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1626?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/434?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly
spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 2019-01-11 https://github.com/ogotoh/spaln 2.4.9 python To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 110 132 399 612 267 318 4249 4506 0 0 0 0 0 0 0 0 5118 4648 450 377
spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. 2024-08-25 https://github.com/theislab/spapros 0.1.5 spapros 0.1.5 Up-to-date Single Cell, Transcriptomics, Sequence Analysis Primer and probe design, Visualisation Primer and probe design, Visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros spapros spapros Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 1 1 https://usegalaxy.eu/published/workflow?id=9adf0402b641042c
spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads 2018-05-07 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping 2.1 Up-to-date Sequence Analysis Variant pattern analysis Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 2042 2042 0 0 0 0 0 0 0 0 0 0 0 0 2042 2042 34 34
spyboat spyboat Wavelet analysis for 3d-image stacks 2020-11-28 http://github.com/tensionhead/spyboat 0.1.2 spyboat To update Imaging, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6 6 174 174 0 0 0 0 0 0 0 0 0 0 0 0 174 174 6 6
squirrel squirrel_phylo, squirrel_qc QC and Phylogenetic analysis of MPXV 2025-01-16 https://github.com/aineniamh/squirrel 1.0.13 squirrel 1.2.2 To update Phylogenetics Phylogenetic analysis, Sequencing quality control Phylogenetic analysis, Sequencing quality control Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel squirrel squirrel Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7 7 0 0 0 0 41 41 193 193 0 0 0 0 200 200 43 43 https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323
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srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.22.1 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 https://workflowhub.eu/workflows/407?version=1
stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2016-03-07 http://catchenlab.life.illinois.edu/stacks/ stacks 2.68 To update Sequence Analysis Data handling Data handling Mapping, Population genetics Mapping, Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 132 199 6924 14189 0 0 0 0 40 40 6127 6127 2 2 8 8 20324 13059 241 174 https://workflowhub.eu/workflows/1662?version=1, https://workflowhub.eu/workflows/1665?version=1, https://workflowhub.eu/workflows/1666?version=1, https://workflowhub.eu/workflows/1683?version=1 ecology/de-novo-rad-seq, ecology/genetic-map-rad-seq, ecology/ref-based-rad-seq
stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2018-12-01 http://catchenlab.life.illinois.edu/stacks/ 2.55 stacks 2.68 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 118 145 8146 11221 0 0 0 0 54 54 22200 22427 8 9 650 651 34299 30996 208 180 https://usegalaxy.eu/published/workflow?id=510bcef37f385495, https://usegalaxy.eu/published/workflow?id=f5d387583670f694, https://usegalaxy.org.au/published/workflow?id=1e71b5232b9b4d2a, https://usegalaxy.org.au/published/workflow?id=9b3f3d331d0b2892, https://usegalaxy.org.au/published/workflow?id=a401ad5349b44dfb, https://usegalaxy.org.au/published/workflow?id=ca45322bff44e73a, https://usegalaxy.org.au/published/workflow?id=f7adc76331620f34, https://workflowhub.eu/workflows/347?version=1, https://workflowhub.eu/workflows/348?version=1, https://workflowhub.eu/workflows/349?version=1, https://workflowhub.eu/workflows/350?version=1, https://workflowhub.eu/workflows/352?version=1
star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR 2015-10-15 https://github.com/STAR-Fusion/STAR-Fusion 0.5.4-3+galaxy1 star-fusion 1.15.1 To update Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 84 108 1268 1483 204 337 1678 3284 4 4 300 300 0 0 0 0 5067 3246 449 292
staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2024-09-19 https://github.com/phac-nml/staramr 0.11.0 staramr 0.11.1 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2921 3072 31443 33124 2130 2130 14763 14763 1173 1182 8989 9237 97 97 9838 9838 66962 65033 6481 6321 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore
straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model 2022-10-02 https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.3 To update Systems Biology, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. 2021-01-27 https://github.com/Illumina/strelka/ 2.9.10 strelka 2.9.10 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 88 88 992 992 342 342 1990 1990 0 0 0 0 0 0 0 0 2982 2982 430 430 https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7
stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. 2014-09-13 http://ccb.jhu.edu/software/stringtie/ 2.2.3 stringtie 3.0.2 To update Transcriptomics Transcriptome assembly, RNA-Seq analysis Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-Seq Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3884 4419 194508 217287 6876 11163 316022 446115 673 865 27958 33201 302 303 3783 3787 700390 542271 16750 11735 https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=0eb137cd936bbfe0, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=1cd85fe90839c10d, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=2287afbf248d9c89, https://usegalaxy.eu/published/workflow?id=249c5d6698c8b98c, https://usegalaxy.eu/published/workflow?id=2d08a73dd8ff99e9, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, 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structure structure for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html 2.3.4 structure 2.3.4 Up-to-date Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 155 3903 4354 0 0 0 0 0 0 0 0 3 3 330 330 4684 4233 158 141
structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method 2017-12-06 http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ 0.6.94 structureharvester 0.6.94 Up-to-date Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. 2021-04-05 https://github.com/wtsi-hpag/PretextSnapshot 0.0.7 pretextgraph 0.0.9 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 397 397 5173 5173 241 241 6703 6703 53 53 1729 1729 0 0 0 0 13605 13605 691 691 https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=44c92c04f1d14631, 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swiftlink swiftlink Parallel MCMC Linkage Analysis 2017-11-21 https://github.com/ajm/swiftlink 1.0 swiftlink 1.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. 2022-06-23 1.0 clustalo 1.2.4 To update Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2
syri syri Synteny and Rearrangement Identifier 2025-04-16 https://github.com/schneebergerlab/syri 1.7.1 syri 1.7.1 Up-to-date Sequence Analysis Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing DNA polymorphism, Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri SyRI SyRI SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 84 84 0 0 0 0 0 0 0 0 5 5 76 76 160 160 27 27 https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef
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tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 507 586 9277 11798 740 2407 7442 32030 92 124 892 1250 11 12 20 22 45100 17631 3129 1350 https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1e1a299825f27f11, https://usegalaxy.org/published/workflow?id=1efb485f123233eb, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5de035c08af915ea, https://usegalaxy.org/published/workflow?id=9304cc9410a96323, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9 single-cell/scrna-data-ingest
tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. 2016-05-05 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup 1.0.2 openjdk To update Statistics, SAM, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 17 35 184 34 77 661 875 0 0 0 0 0 0 0 0 1059 696 94 45
tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches 2020-04-19 https://github.com/nebiolabs/tasmanian-mismatch 1.0.9 tasmanian-mismatch 1.0.9 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 23 23 32 32 292 292 0 0 0 0 0 0 0 0 315 315 43 43 https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702, https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f
taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit 2024-07-26 https://bioinf.shenwei.me/taxonkit/ 0.20.0 taxonkit 0.20.0 Up-to-date Metagenomics Formatting, Data retrieval Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Taxonomy, Biotechnology, Ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 1094 1094 0 0 0 0 0 0 0 0 0 0 0 0 1094 1094 12 12 https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1
taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy 2019-01-13 https://github.com/pvanheus/ncbitaxonomy 0.3.0 rust-ncbitaxonomy 1.0.7 To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile 2015-08-06 http://sourceforge.net/projects/krona/ 2.7.1+galaxy0 krona 2.8.1 To update Assembly Visualisation Visualisation Metagenomics Metagenomics crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 7406 7874 48617 51653 6438 7659 33268 41191 2005 2042 11003 11192 162 163 565 586 104622 93453 17738 16011 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, 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taxpasta taxpasta standardise taxonomic profiles 2023-08-30 https://taxpasta.readthedocs.io/en/latest/ 0.7.0 taxpasta 0.7.0 Up-to-date Sequence Analysis Standardisation and normalisation, Aggregation, Formatting, Conversion Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 323 323 0 0 0 0 0 0 0 0 1 1 18 18 341 341 52 52 https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7
tb-profiler tb_profiler_collate, tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. 2019-04-02 https://github.com/jodyphelan/TBProfiler 6.6.5 tb-profiler 6.6.5 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 491 535 15947 16201 490 506 11483 11641 199 201 10939 10981 0 0 0 0 38823 38369 1242 1180 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1564?version=1, https://workflowhub.eu/workflows/1647?version=1 evolution/mtb_transmission, variant-analysis/tb-variant-analysis
tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter 2019-10-03 https://github.com/COMBAT-TB/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 618 655 43892 44301 356 364 23229 23483 103 103 10184 10203 1 1 3000 3000 80987 80305 1123 1078 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1569?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1647?version=1 evolution/mtb_transmission, variant-analysis/tb-variant-analysis
tbl2gff3 tbl2gff3 Table to GFF3 2020-07-07 https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 661 661 2492 2492 255 255 604 604 148 148 649 649 17 17 53 53 3798 3798 1081 1081 https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation
tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) 2019-08-29 https://github.com/COMBAT-TB/tbvcfreport 1.0.1 tbvcfreport 1.0.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 378 411 9773 9913 418 441 7332 7415 96 97 3675 3682 1 1 1 1 21011 20781 950 893 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1647?version=1 variant-analysis/tb-variant-analysis
te_finder te_finder Transposable element insertions finder 2022-08-08 https://github.com/VistaSohrab/TEfinder 1.0.1 samtools 1.22.1 To update Sequence Analysis Genome indexing, Variant calling, PCR primer design Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 28 28 219 219 0 0 0 0 0 0 0 0 0 0 0 0 219 219 28 28
telescope_assign telescope_assign Single locus resolution of Transposable ELEment expression. 2019-09-03 https://github.com/mlbendall/telescope/ 1.0.3 telescope 1.0.3 Up-to-date Genome annotation Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tesseract tesseract Tesseract is an OCR engine with support for unicode and the ability to recognize more than 100 languages out of the box. 2025-06-18 https://github.com/tesseract-ocr/tesseract 5.5.1 tesseract 3.04.01 To update Natural Language Processing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tesseract https://github.com/galaxyproject/tools-iuc/tree/main/tools/tesseract 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 83 83 0 0 0 0 0 0 0 0 0 0 0 0 83 83 10 10
tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. 2020-04-10 https://github.com/mhammell-laboratory/TEtranscripts 2.2.3 tetranscripts 2.2.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 93 1167 1200 0 0 0 0 5 5 206 206 0 0 0 0 1406 1373 98 94
tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. 2019-11-23 https://github.com/aesheppard/TETyper 1.1 tetyper 1.1 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 25 146 178 50 57 142 200 0 0 0 0 0 0 0 0 378 288 82 73
tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences 2018-06-06 https://github.com/veg/tn93/ 1.0.15 tn93 1.0.15 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 31 31 1952 1952 86 102 2566 2831 0 0 0 0 0 0 0 0 4783 4518 133 117
tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files 2024-04-30 https://gitlab.com/ifb-elixirfr/abromics/tooldistillator 1.0.1 tooldistillator 1.0.1 Up-to-date Sequence Analysis Data parsing Microbiology, Bioinformatics, Sequence analysis Microbiology, Bioinformatics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 121 5042 5042 162 162 1550 1550 0 0 0 0 9 9 19253 19253 25845 25845 292 292 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tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. 2024-03-28 https://github.com/cbib/TraceGroomer 0.1.4 tracegroomer 0.1.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 16 16 0 0 0 0 0 0 0 0 4 4 42 42 58 58 6 6 https://usegalaxy.fr/published/workflow?id=879408d684923861
tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose A suite tools for basecalling, alignment, assembly and deconvolution of Sanger chromatograms using tracy. 2021-10-12 https://github.com/gear-genomics/tracy/ 0.7.8 tracy 0.8.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 55 55 4837 4837 0 0 0 0 0 0 0 0 0 0 0 0 4837 4837 55 55
transdecoder transdecoder TransDecoder finds coding regions within transcripts 2015-11-09 https://transdecoder.github.io/ 5.5.0 transdecoder 5.7.1 To update Transcriptomics, RNA Coding region prediction, de Novo sequencing, De-novo assembly Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1215 1323 7178 8593 1267 1357 6450 7010 372 432 3197 3705 37 38 495 505 19813 17320 3150 2891 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.org.au/published/workflow?id=c04a62f528a69e79, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://workflowhub.eu/workflows/1716?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1, https://workflowhub.eu/workflows/879?version=1 transcriptomics/full-de-novo
transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT 2019-03-01 https://github.com/mad-lab/transit/ 3.2.3 transit 3.3.19 To update Genome annotation Transposon prediction Transposon prediction DNA, Sequencing, Mobile genetic elements DNA, Sequencing, Mobile genetic elements iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 97 104 1908 2076 210 244 2813 4134 42 42 640 640 0 0 0 0 6850 5361 390 349 https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://workflowhub.eu/workflows/1530?version=1 genome-annotation/tnseq
transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes 2015-10-08 https://transterm.cbcb.umd.edu transtermhp 2.09 To update Sequence Analysis Transcriptional regulatory element prediction Transcriptional regulatory element prediction Transcription factors and regulatory sites Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 62 467 502 49 55 170 216 0 0 0 0 0 0 0 0 718 637 117 108
trimal trimal Tool for automated alignment trimming 2024-10-02 https://trimal.readthedocs.io 1.5.0 trimal 1.5.0 Up-to-date Sequence Analysis, Phylogenetics Multiple sequence alignment Multiple sequence alignment Sequence analysis, Sequencing, Sequence sites, features and motifs Sequence analysis, Sequencing, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal trimal trimAl Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 173 173 2180 2180 0 0 0 0 4 4 32 32 115 115 1230 1230 3442 3442 292 292 https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6, https://workflowhub.eu/workflows/1650?version=1 sequence-analysis/tapscan-streptophyte-algae
trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data 2024-01-03 http://www.usadellab.org/cms/?page=trimmomatic 0.39 trimmomatic 0.40 To update Fastq Manipulation pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 18851 20991 437833 502595 45190 60956 714562 1020864 6132 7428 144168 173860 1010 1011 37524 37543 1734862 1334087 90386 71183 https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=0d6bed63a2e4c3d6, https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792, 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https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1606?version=1, https://workflowhub.eu/workflows/1651?version=1, https://workflowhub.eu/workflows/1653?version=1, https://workflowhub.eu/workflows/1678?version=1, https://workflowhub.eu/workflows/1685?version=1, https://workflowhub.eu/workflows/1716?version=1, https://workflowhub.eu/workflows/1767?version=1, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/676?version=1, https://workflowhub.eu/workflows/876?version=1 epigenetics/tal1-binding-site-identification, evolution/mtb_transmission, microbiome/mgnify-amplicon, sequence-analysis/human-reads-removal, transcriptomics/de-novo, transcriptomics/full-de-novo, variant-analysis/exome-seq, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants
trimns trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline 2021-01-29 https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs 0.1.0 trimns_vgp 1.0 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 25 25 49 49 0 0 0 0 0 0 0 0 0 0 0 0 49 49 25 25
trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq 2015-11-09 https://github.com/trinityrnaseq/trinityrnaseq 2.15.1 trinity 2.15.2 To update Transcriptomics, RNA Transcriptome assembly Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Transcriptomics, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. 9 13 13 13 0 0 0 0 0 0 0 0 0 0 3 2 1 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 2033 2319 42409 52163 3769 4091 48710 53240 809 933 22208 30291 155 159 3279 3411 139105 116606 7502 6766 https://workflowhub.eu/workflows/1716?version=1 transcriptomics/full-de-novo
trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. 2016-11-15 https://trinotate.github.io/ 3.2.2 trinotate 4.0.2 To update Transcriptomics, RNA Gene functional annotation Gene functional annotation Gene expression, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 458 517 2157 2558 549 598 2012 2211 170 224 950 1284 0 1 0 10 6063 5119 1340 1177 https://workflowhub.eu/workflows/1716?version=1 transcriptomics/full-de-novo
trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers 2021-02-11 https://github.com/rrwick/Trycycler 0.5.5 trycycler 0.5.6 To update Assembly Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler trycycler Trycycler Trycycler: consensus long-read assemblies for bacterial genomes 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 122 122 15743 15743 0 0 0 0 57 57 6233 6233 3 3 27 27 22003 22003 182 182
tsebra tsebra This tool has been developed to combine BRAKER predictions. 2023-10-19 https://github.com/Gaius-Augustus/TSEBRA 1.1.2.5 tsebra 1.1.2.5 Up-to-date Genome annotation Homology-based gene prediction, Alternative splicing prediction Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Gene expression, RNA-Seq, Gene transcripts, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 51 51 0 0 0 0 0 0 0 0 0 0 0 0 51 51 16 16
tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation 2017-05-26 https://cran.r-project.org/web/packages/Rtsne/ 0.0.2 r-rtsne 0.13 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 25 39 163 382 60 69 275 305 0 0 0 0 2 2 4 4 691 442 110 87
tximport tximport Wrapper for the Bioconductor package tximport 2019-10-15 http://bioconductor.org/packages/tximport/ 1.30.0 bioconductor-tximport 1.34.0 To update Transcriptomics Pathway or network analysis, Formatting, RNA-Seq analysis Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Transcriptomics, Gene transcripts, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 297 314 2388 2576 994 1081 7694 8341 0 0 0 0 0 0 0 0 10917 10082 1395 1291 https://usegalaxy.eu/published/workflow?id=65aed668233d5f73
ucsc_axtchain ucsc_axtchain Chain together genome alignments 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-axtchain 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 57 57 0 0 0 0 0 0 0 0 57 57 4 4
ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-axttomaf 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 59 59 0 0 0 0 0 0 0 0 59 59 4 4
ucsc_blat ucsc_blat Standalone blat sequence search command line tool 2017-05-17 http://genome.ucsc.edu/goldenPath/help/blatSpec.html 482 ucsc-blat 482 Up-to-date Sequence Analysis Sequence alignment Sequence alignment Sequence analysis Sequence analysis yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat blat BLAT Fast, accurate spliced alignment of DNA sequences. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_chainantirepeat ucsc_chainantirepeat Remove repeated chains 2025-03-07 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-chainantirepeat 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 42 42 0 0 0 0 0 0 0 0 42 42 3 3
ucsc_chainnet ucsc_chainnet Make alignment nets out of chains 2024-08-30 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-chainnet 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 61 61 0 0 0 0 0 0 0 0 61 61 4 4
ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-chainprenet 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 60 60 0 0 0 0 0 0 0 0 60 60 4 4
ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-chainsort 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 60 60 0 0 0 0 0 0 0 0 60 60 4 4
ucsc_fasplit fasplit faSplit is a tool to split a single FASTA file into several files 2017-09-08 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-fasplit 482 Up-to-date Fasta Manipulation Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 602 3994 4315 689 777 6770 7638 212 218 1497 1540 8 8 38 38 13531 12299 1605 1463 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org.au/published/workflow?id=8ae08ac9e73c8241
ucsc_fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs 2023-01-11 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-fatovcf 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 515 515 205 205 1868 1868 13 13 226 226 0 0 0 0 2609 2609 290 290 https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 variant-analysis/pox-tiled-amplicon
ucsc_maftoaxt maftoaxt Convert dataset from MAF to axt format 2024-07-30 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-maftoaxt 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 11 11 0 0 0 0 0 0 0 0 11 11 3 3
ucsc_netfilter ucsc_netfilter Filter out parts of net 2024-09-18 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-netfilter 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 56 56 0 0 0 0 0 0 0 0 56 56 4 4
ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset 2024-09-04 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-netsyntenic 482 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 72 72 0 0 0 0 0 0 0 0 72 72 6 6
ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. 2024-09-19 http://hgdownload.cse.ucsc.edu/admin/exe/ 482 ucsc-nettoaxt 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 55 55 0 0 0 0 0 0 0 0 55 55 4 4
ucsc_twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA 2016-08-19 https://genome.ucsc.edu/goldenpath/help/twoBit.html 482 ucsc-twobittofa 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 85 126 430 570 131 159 803 861 3 3 73 73 0 0 0 0 1504 1306 288 219
ucsc_wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig 2024-01-14 https://genome.ucsc.edu/goldenPath/help/bigWig.html 482 ucsc-wigtobigwig 482 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 345 345 4562 4562 759 759 9257 9257 58 58 1088 1088 0 0 0 0 14907 14907 1162 1162 https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=4ca06bc64bf896a3, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org/published/workflow?id=28e4871410288cb8, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee
umi-tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq 2017-08-09 https://github.com/CGATOxford/UMI-tools 1.1.6 umi_tools 1.1.6 Up-to-date Sequence Analysis, Transcriptomics, Single Cell Sequencing quality control Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Sequence sites, features and motifs, Quality affairs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 1 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 568 710 48490 74207 637 637 12544 12796 109 118 17752 18006 5 5 48 48 105057 78834 1470 1319 https://usegalaxy.eu/published/workflow?id=06fe33c4420906bf, https://usegalaxy.eu/published/workflow?id=0821ec1cb4d6f30b, https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=26185e8fa5a9b988, https://usegalaxy.eu/published/workflow?id=44c5999436da5f1e, https://usegalaxy.eu/published/workflow?id=49073a24429d93d6, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=a1e09c648d8f1fc7, https://usegalaxy.eu/published/workflow?id=af7c349497a75314, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=c64b219b4031fabd, https://usegalaxy.eu/published/workflow?id=c6b22fc33b569c8f, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044, https://usegalaxy.eu/published/workflow?id=d7aa4c258e2edc95, https://usegalaxy.eu/published/workflow?id=edbdbe7aa21ceba0, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.eu/published/workflow?id=f841e1207611f28f, https://usegalaxy.org.au/published/workflow?id=7ae06a27188b9438, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://workflowhub.eu/workflows/1494?version=1, https://workflowhub.eu/workflows/1507?version=1, https://workflowhub.eu/workflows/1706?version=1 single-cell/scrna-preprocessing, single-cell/scrna-umis, transcriptomics/clipseq
unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. 2017-05-08 https://github.com/rrwick/Unicycler 0.5.1 unicycler 0.5.1 Up-to-date Assembly Genome assembly, Aggregation Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Microbiology, Genomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4697 5202 83521 96874 5770 8769 65067 104850 2392 2613 22717 26831 272 276 2160 2183 230738 173465 16860 13131 https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=8b8e89b9b8801f2f, https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=fe43cf59e48bf556, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=a67afbea4b2eb26b, https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d, https://usegalaxy.org/published/workflow?id=bc72dcbca89ca35d, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=db0671862a57968d, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1598?version=1, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 assembly/assembly-with-preprocessing, assembly/unicycler-assembly, microbiome/plasmid-metagenomics-nanopore
upsetplot rcx_upsetplot Upset plot visualization tool using UpSetR 2025-04-17 https://github.com/galaxyproject/tools-iuc 1.4.0 r-upsetr 1.0.3 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
usher usher_matutils, usher UShER toolkit wrappers 2021-05-11 https://github.com/yatisht/usher 0.2.1 usher 0.6.6 To update Phylogenetics Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics Cladistics, Genotype and phenotype, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 5 5 1060 1060 0 0 0 0 0 0 0 0 0 0 0 0 1060 1060 5 5
valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 74 101 449 711 67 76 160 249 0 0 0 0 0 0 0 0 960 609 177 141 https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09
vapor vapor Classify Influenza samples from raw short read sequence data 2022-08-24 https://github.com/wm75/vaporup 1.0.3 vapor 1.0.3 Up-to-date Sequence Analysis Data retrieval, De-novo assembly, Read mapping Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Whole genome sequencing, Mapping, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 188 188 197466 197466 127 127 1849 1849 0 0 0 0 0 0 0 0 199315 199315 315 315 https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://workflowhub.eu/workflows/1260?version=2 variant-analysis/aiv-analysis
vardict_java vardict_java VarDict - calls SNVs and indels for tumour-normal pairs 2020-08-21 https://github.com/AstraZeneca-NGS/VarDictJava 1.8.3 python To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 48 49 409 424 0 0 0 0 0 0 0 0 0 0 0 0 424 409 49 48 https://workflowhub.eu/workflows/1738?version=1, https://workflowhub.eu/workflows/1739?version=1, https://workflowhub.eu/workflows/1740?version=1, https://workflowhub.eu/workflows/1741?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1
variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data 2019-11-20 2.0.0 matplotlib To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 5 6 54 99 26 29 221 557 0 0 0 0 0 0 0 0 656 275 35 31
varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data 2018-07-10 https://dkoboldt.github.io/varscan/ 2.4.3 varscan 2.4.6 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 813 965 13818 16510 2269 2508 18111 19895 101 101 1552 1552 288 288 1010 1010 38967 34491 3862 3471 https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=231a2dc7412d250b, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=462582bbc236cb7b, https://usegalaxy.eu/published/workflow?id=4f62794453f65cba, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=83049910e2cd5128, https://usegalaxy.eu/published/workflow?id=88064e2231165fd2, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a4e3667f6879bfaf, https://usegalaxy.eu/published/workflow?id=af30010868c97316, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.org/published/workflow?id=0ee0493f3168cbb3, https://usegalaxy.org/published/workflow?id=18c6e87a884fb5ed, https://usegalaxy.org/published/workflow?id=3dbe754882a263cd, https://usegalaxy.org/published/workflow?id=4cbb8181cfdf55d9, https://usegalaxy.org/published/workflow?id=7c5e8394ce29288d, https://usegalaxy.org/published/workflow?id=bf90f2bd20fbff21, https://workflowhub.eu/workflows/1678?version=1, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/628?version=1 variant-analysis/somatic-variants
varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses 2024-01-27 https://github.com/jonas-fuchs/varVAMP/ 1.2.2 varvamp 1.2.2 Up-to-date Sequence Analysis PCR primer design PCR primer design Virology, Probes and primers Virology, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 55 912 912 0 0 0 0 0 0 0 0 0 0 0 0 912 912 55 55 https://workflowhub.eu/workflows/1627?version=1 sequence-analysis/viral_primer_design
vcf2maf vcf2maf vcf2maf: Convert VCF into MAF 2022-06-28 https://github.com/mskcc/vcf2maf 1.6.21 vcf2maf 1.6.22 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 1688 1688 0 0 0 0 7 7 179 179 0 0 0 0 1867 1867 71 71 https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1
vcf2tsv vcf2tsv Converts VCF files into tab-delimited format 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1000 1110 178652 180838 1122 2888 17000 45505 165 203 4866 5129 72 73 252 254 231726 200770 4274 2359 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31, https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb, https://usegalaxy.eu/published/workflow?id=3d8aa05129e44fdf, https://usegalaxy.eu/published/workflow?id=4d80a87510b2a54e, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b, https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8, https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.org.au/published/workflow?id=2362ff8880213586, https://usegalaxy.org.au/published/workflow?id=3e6f755ee62f7301, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2, https://usegalaxy.org/published/workflow?id=415c7152cb78e86f, https://usegalaxy.org/published/workflow?id=43861b38cf6e927e, https://usegalaxy.org/published/workflow?id=4dbac8374419d29e, https://usegalaxy.org/published/workflow?id=4ed9f54caa932479, https://usegalaxy.org/published/workflow?id=50206b10de958d03, https://usegalaxy.org/published/workflow?id=57cfc1b5d9ea0d72, https://usegalaxy.org/published/workflow?id=5cad854edbbd3b69, https://usegalaxy.org/published/workflow?id=68d41ffbf92b2a8e, https://usegalaxy.org/published/workflow?id=bb16936081b820f6, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://workflowhub.eu/workflows/1628?version=1, https://workflowhub.eu/workflows/1659?version=1 variant-analysis/baculovirus-isolate-variation, variant-analysis/non-dip
vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 858 1007 36 118 6132 9104 7 7 184 237 0 0 0 0 10348 7174 157 69
vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 918 1372 7607 21544 1134 2095 6447 15257 234 280 3141 3515 4 6 4 8 40324 17199 3753 2290 https://usegalaxy.eu/published/workflow?id=2f1ee01aeee2b9f0, https://usegalaxy.eu/published/workflow?id=4a89ddab941c6819, https://usegalaxy.eu/published/workflow?id=a4e3667f6879bfaf, https://usegalaxy.eu/published/workflow?id=ad609d1a3de251f5, https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730, https://usegalaxy.eu/published/workflow?id=ffe93ec81afefd09, https://usegalaxy.org.au/published/workflow?id=738c0e8227519c25, https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c, https://usegalaxy.org/published/workflow?id=70dacee3da375e2b, https://workflowhub.eu/workflows/1655?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1 variant-analysis/dip
vcfanno vcfanno Annotate VCF files 2021-01-17 https://github.com/brentp/vcfanno 0.3.7 vcfanno 0.3.7 Up-to-date Variant Analysis SNP annotation SNP annotation Genetic variation, Data submission, annotation and curation Genetic variation, Data submission, annotation and curation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 239 239 1308 1308 0 0 0 0 0 0 0 0 0 0 0 0 1308 1308 239 239 https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1
vcfannotate vcfannotate Intersect VCF records with BED annotations 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 206 2810 3070 627 1507 3510 14904 61 69 604 730 5 6 13 14 18718 6937 1788 854 https://usegalaxy.org.au/published/workflow?id=142e5f7c1f340838, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org/published/workflow?id=3e2bbafb8c6580af
vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 73 114 218 133 403 404 1863 13 13 199 253 1 1 3 3 2337 720 490 204
vcfbedintersect vcfbedintersect Intersect VCF and BED datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 251 3039 4433 423 1241 4483 21130 42 47 546 658 2 3 17 22 26243 8085 1542 675 https://usegalaxy.org/published/workflow?id=6da54816b436dc58, https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99
vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 40 265 478 61 320 3591 10654 7 8 386 485 0 1 0 1 11618 4242 369 97 https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99
vcfcheck vcfcheck Verify that the reference allele matches the reference genome 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 109 128 1560 1680 207 669 754 2025 18 19 401 461 1 1 1 1 4167 2716 817 335 https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
vcfcombine vcfcombine Combine multiple VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337 585 1639 2560 996 2856 4286 20198 59 74 481 585 6 6 13 13 23356 6419 3521 1398 https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378, https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7, https://usegalaxy.org/published/workflow?id=2478426a119d9d93, https://usegalaxy.org/published/workflow?id=2d44e2b020bf94f8, https://usegalaxy.org/published/workflow?id=865d2cc4d14ec7e1, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=d3e656ab45f40c11, https://usegalaxy.org/published/workflow?id=d43b771d93f0f609, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a
vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 36 49 81 270 78 297 211 1889 10 13 217 282 3 3 15 15 2456 524 362 127
vcfdistance vcfdistance Calculate distance to the nearest variant. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 106 520 648 135 322 1960 2480 21 24 303 368 2 2 2 2 3498 2785 454 254
vcffilter vcffilter2 Tool for filtering VCF files 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2682 2972 41687 54337 5382 11813 62117 173095 319 406 3130 3934 53 53 266 266 231632 107200 15244 8436 https://usegalaxy.eu/published/workflow?id=22454322d370b3ff, https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb, https://usegalaxy.eu/published/workflow?id=2a13eb981d6ee36e, https://usegalaxy.eu/published/workflow?id=3b7c0b64033f38ac, https://usegalaxy.eu/published/workflow?id=533819bcb5aa78c5, https://usegalaxy.eu/published/workflow?id=591ebf913450f49e, https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b, https://usegalaxy.eu/published/workflow?id=5e3c352233aa7a52, 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vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 177 208 1003 1179 282 1037 2113 5539 26 34 252 322 1 1 1 1 7041 3369 1280 486
vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24 32 67 194 68 218 360 988 12 16 193 393 1 1 50 50 1625 670 267 105
vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 117 134 791 900 192 549 2408 3817 22 26 243 308 2 2 4 4 5029 3446 711 333 https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a
vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 142 171 1337 1568 246 900 3621 6730 23 26 231 291 1 1 6 6 8595 5195 1098 412 https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4
vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 279 2002 2396 183 682 1967 4292 19 27 584 754 3 3 12 12 7454 4565 991 466 https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4
vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 42 52 616 740 85 301 345 1145 9 16 188 270 1 2 1 2 2157 1150 371 137 https://usegalaxy.org/published/workflow?id=2478426a119d9d93
vcfprimers vcfprimers Extract flanking sequences for each VCF record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 39 450 722 68 215 324 880 10 13 197 267 1 1 3 3 1872 974 268 108
vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 17 20 89 186 27 81 111 361 6 6 194 243 0 0 0 0 790 394 107 50
vcfselectsamples vcfselectsamples Select samples from a VCF file 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 77 102 786 973 179 989 923 6360 22 24 349 427 0 0 0 0 7760 2058 1115 278 https://usegalaxy.org/published/workflow?id=63e0dcf18794dbc1, https://usegalaxy.org/published/workflow?id=67e56a9919ed84f7, https://usegalaxy.org/published/workflow?id=9b4323b68f609e06, https://usegalaxy.org/published/workflow?id=ad6143e2f74e1e94, https://usegalaxy.org/published/workflow?id=db8443163482a2e0, https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99
vcfsort vcfsort Sort VCF dataset by coordinate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 209 236 1958 2132 413 1369 12476 25718 79 89 597 785 4 4 74 74 28709 15105 1698 705 https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org/published/workflow?id=50206b10de958d03, https://usegalaxy.org/published/workflow?id=bb16936081b820f6, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72
vcfvcfintersect vcfvcfintersect Intersect two VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.14 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 874 977198 979857 916 2249 64595 84741 232 244 18029 21296 15 16 1681 1682 1087576 1061503 3383 1931 https://usegalaxy.eu/published/workflow?id=0882300f7b399587, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=52bdf400f97c5770, https://usegalaxy.eu/published/workflow?id=53de0e742573e588, https://usegalaxy.eu/published/workflow?id=579dd1e95e76402f, https://usegalaxy.eu/published/workflow?id=6dbac47941a804da, https://usegalaxy.eu/published/workflow?id=a6f4371ef9bc1aab, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=ed20bd120064bab0, https://usegalaxy.eu/published/workflow?id=ee6dc47660540ba6, https://usegalaxy.eu/published/workflow?id=fc216dfb0ec9ed41, https://usegalaxy.eu/published/workflow?id=fcf745185d6e0ea4, https://usegalaxy.fr/published/workflow?id=7d27dd394b921846, https://usegalaxy.fr/published/workflow?id=98529cff0ef36b91, https://usegalaxy.fr/published/workflow?id=d0d12c0b80c286f9, https://usegalaxy.fr/published/workflow?id=e0b225d4b2556365, https://usegalaxy.org.au/published/workflow?id=094a545d44ce28cc, https://usegalaxy.org.au/published/workflow?id=2b2ce7e1206d177d, https://usegalaxy.org.au/published/workflow?id=3223ceaa2b58d940, https://usegalaxy.org.au/published/workflow?id=3c657dd766d02f6a, https://usegalaxy.org.au/published/workflow?id=52b6fe5af4911b1a, https://usegalaxy.org.au/published/workflow?id=7fd58f5fc93f414e, https://usegalaxy.org.au/published/workflow?id=810242a3dc4f6170, https://usegalaxy.org.au/published/workflow?id=888eb87b62c4e6dd, https://usegalaxy.org.au/published/workflow?id=baa763dbdf6afb71, https://usegalaxy.org.au/published/workflow?id=bcf230e526632064, https://usegalaxy.org.au/published/workflow?id=be9213411c520096, https://usegalaxy.org.au/published/workflow?id=c1ce3f2ae7c81c3e, https://usegalaxy.org.au/published/workflow?id=c9156ca3df2b595c, https://usegalaxy.org.au/published/workflow?id=d35d05be576e8b13, https://usegalaxy.org.au/published/workflow?id=e439a0e17a90d24c, https://usegalaxy.org.au/published/workflow?id=fe5542c99cdc57ce, https://usegalaxy.org/published/workflow?id=21a047a4e068860f, https://usegalaxy.org/published/workflow?id=262ab42118016c41, https://usegalaxy.org/published/workflow?id=4cf8cc42e97b2da6, https://usegalaxy.org/published/workflow?id=6b11d738ee57f245, https://usegalaxy.org/published/workflow?id=7dde0721a382ea3e, https://usegalaxy.org/published/workflow?id=7e2651e5ed17e3db, https://usegalaxy.org/published/workflow?id=98b2ac8fc75781f8, https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99, https://usegalaxy.org/published/workflow?id=9e487f763daa66c0, https://usegalaxy.org/published/workflow?id=9fc9f1db50019929, https://usegalaxy.org/published/workflow?id=a98a3ac1a41752bc, https://usegalaxy.org/published/workflow?id=b34ba9b2e4d8f050, https://usegalaxy.org/published/workflow?id=b461ac6f18e0c9cf, https://usegalaxy.org/published/workflow?id=bd355e8ce58a139e, https://usegalaxy.org/published/workflow?id=bf3ccae8d5b6ef58, https://usegalaxy.org/published/workflow?id=d196c3bde666eccb, https://usegalaxy.org/published/workflow?id=d4ea6cdd40522eb1, https://usegalaxy.org/published/workflow?id=e282f505ba9f729f, https://usegalaxy.org/published/workflow?id=e2c77aeabb8053b4, https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://workflowhub.eu/workflows/110?version=11
vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 101 116 2314 2547 167 318 3493 5788 0 0 0 0 0 0 0 0 8335 5807 434 268
velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. 2021-04-30 http://velocyto.org/ 0.17.17 velocyto.py 0.17.17 Up-to-date Transcriptomics, Single Cell RNA-Seq analysis, Splicing analysis RNA-Seq analysis, Splicing analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto velocyto Velocyto Estimating RNA velocity in single cell RNA sequencing datasets 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 131 131 12 12 75 75 1 1 192 192 0 0 0 0 398 398 27 27 https://usegalaxy.eu/published/workflow?id=c5841e0458a4ebf7, https://usegalaxy.eu/published/workflow?id=c58bb47e04157ee6, https://usegalaxy.org.au/published/workflow?id=1e5a77d9e9630115, https://usegalaxy.org.au/published/workflow?id=77e0ca6492f40c9c, https://usegalaxy.org/published/workflow?id=29d51c37d66deeeb, https://usegalaxy.org/published/workflow?id=6592430b80345167
velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 2567 2888 27621 32158 4951 5263 52855 57273 2097 2221 30746 33121 109 109 1097 1097 123649 112319 10481 9724 https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=30430b75d05f54eb, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org.au/published/workflow?id=7fa13ccbf044edc5, https://usegalaxy.org.au/published/workflow?id=83e3ceceb1a92493, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=8b6739a000780d99, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org.au/published/workflow?id=ee7a1615f187391d, https://usegalaxy.org.au/published/workflow?id=f25a05070bf97ded, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f6bd33dedc7c6c12, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/1622?version=1 assembly/general-introduction
velvetoptimiser velvetoptimiser Automatically optimize Velvet assemblies 2017-12-19 2.2.6+galaxy2 velvet 1.2.10 To update Assembly Optimisation and refinement, Sequence assembly Optimisation and refinement, Sequence assembly Genomics, Sequence assembly Genomics, Sequence assembly simon-gladman https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 968 1161 4741 6009 2238 2532 9434 10734 849 1433 2848 5743 0 0 0 0 22486 17023 5126 4055 https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=8d47811c6154d347, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://workflowhub.eu/workflows/1626?version=1 assembly/debruijn-graph-assembly
verkko verkko Telomere-to-telomere assembly pipeline 2023-01-24 https://github.com/marbl/verkko 1.3.1 verkko 2.2.1 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 105 105 0 0 0 0 13 13 136 136 0 0 0 0 241 241 56 56
vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods 2020-04-08 https://github.com/vgteam/vg 1.23.0 vg 1.67.0 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 12 15 15 480 0 0 0 0 0 0 0 0 0 0 0 0 480 15 15 12 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40
viralverify viralverify Contigs prediction as viral, chromosomal, plasmidic or uncertain. 2025-07-04 https://github.com/ablab/viralVerify 1.1 viralverify 1.1 Up-to-date Sequence Analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers 2025-08-04 https://github.com/marieBvr/virAnnot 1.2.0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot virannot virAnnot VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 336 336 0 0 0 0 0 0 0 0 2 2 14 14 350 350 18 18 https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c
virheat virheat generates a heatmap of allele frequencies from vcf files 2024-05-15 https://github.com/jonas-fuchs/virHEAT 0.7.1 virheat 0.7.6 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 29 29 0 0 0 0 0 0 0 0 0 0 0 0 29 29 7 7
virhunter virhunter Deep Learning method for novel virus detection in sequencing data 2022-09-13 https://github.com/cbib/virhunter 1.0.0 numpy To update Machine Learning Sequence classification Sequence classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 1700 1700 0 0 0 0 0 0 0 0 0 0 0 0 1700 1700 121 121
virulign virulign A tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins. 2025-08-14 https://github.com/rega-cev/virulign 1.1.1 virulign 1.1.1 Up-to-date RNA, Sequence Analysis, Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virulign https://github.com/galaxyproject/tools-iuc/tree/main/tools/virulign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
volcanoplot volcanoplot Tool to create a Volcano Plot 2018-10-01 https://ggplot2.tidyverse.org/ 4.0.0 r-ggplot2 2.2.1 To update Visualization, Transcriptomics, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4591 5038 38589 45177 6962 7279 66385 70667 1001 1068 8606 9348 266 267 1555 1558 126750 115135 13652 12820 https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=350d7e6976e15d30, https://usegalaxy.eu/published/workflow?id=3ac10b9887fd0fb2, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=68e8042f11d5a3fd, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.eu/published/workflow?id=81f1927bfe3ffea1, https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=8b1e2fe9f4a07de0, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=bc79a9f797334b01, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=d41b52a15ba56f54, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.eu/published/workflow?id=e7363b9f450c56b4, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=f58526da1fd68108, https://usegalaxy.eu/published/workflow?id=fd156028b09d213a, https://usegalaxy.org.au/published/workflow?id=04ab43fb3e7840ef, https://usegalaxy.org.au/published/workflow?id=28705b86e0595ded, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org.au/published/workflow?id=897e9d7432d231e9, https://usegalaxy.org.au/published/workflow?id=8eab5e2b2c683076, https://usegalaxy.org.au/published/workflow?id=9988bc2402f32dc1, https://usegalaxy.org.au/published/workflow?id=a8d9a16eea69b812, https://usegalaxy.org.au/published/workflow?id=a9e59d38c6c710bc, https://usegalaxy.org/published/workflow?id=0930f955bdac93e8, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=25cdc47baba556c5, https://usegalaxy.org/published/workflow?id=40a65b5bc1dcc0b4, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=4c840284d2984fa0, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=667493d318b86b7d, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=7497bfdd2085b6e0, https://usegalaxy.org/published/workflow?id=b0e19e7315b64c87, https://usegalaxy.org/published/workflow?id=e40c2e7f6b73fb11, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1556?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1709?version=1 genome-annotation/crispr-screen, single-cell/pseudobulk-analysis, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-viz-with-volcanoplot, transcriptomics/rna-seq-viz-with-volcanoplot-r
vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.30.1 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. 8 8 8 8 0 0 0 0 0 0 0 0 0 0 8 8 8 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 226 259 13600 15795 323 642 14828 59476 82 97 6641 7811 11 12 285 286 83368 35354 1010 642 https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1
vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. 2020-04-26 https://github.com/USDA-VS/vSNP 3.0.6 pysam 0.23.3 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
weblogo3 rgweblogo3 Sequence Logo generator for fasta 2017-11-17 3.5.0 weblogo 3.7.9 To update Graphics Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis Nucleic acid sites, features and motifs, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 weblogo WebLogo Web-based application designed to make generate sequence logos. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 305 344 3638 3856 1198 3777 8383 31758 52 69 577 1423 10 10 40 40 37077 12638 4200 1565 https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7
windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker 2023-12-14 https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ 1.0 blast 2.17.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 23 856 856 14 14 609 609 3 3 807 807 0 0 0 0 2272 2272 40 40 https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347
winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. 2021-04-29 https://github.com/marbl/Winnowmap 2.03 winnowmap 2.03 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 54 54 317 317 19 19 90 90 0 0 0 0 0 0 0 0 407 407 73 73 https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656
xpath xpath XPath XML querying tool 2015-04-14 http://search.cpan.org/dist/XML-XPath/ perl-xml-xpath 1.47 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 10 30 248 0 1 0 1 0 0 0 0 0 0 0 0 249 30 11 8 https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf
yahs yahs Yet Another Hi-C scaffolding tool 2022-06-28 https://github.com/c-zhou/yahs 1.2a.2 yahs 1.2.2 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 291 291 2516 2516 107 107 750 750 41 41 1062 1062 0 0 0 0 4328 4328 439 439 https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=44c92c04f1d14631, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, 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https://usegalaxy.org/published/workflow?id=a8cd62e1924a64e1, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=c95e9116e4b7982b, https://usegalaxy.org/published/workflow?id=f09033420c6267ab, https://usegalaxy.org/published/workflow?id=fa36d9b50e956917, https://usegalaxy.org/published/workflow?id=fb98ef955b3dbd4b, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=27, https://workflowhub.eu/workflows/702?version=1 assembly/vgp_genome_assembly
zerone zerone ChIP-seq discretization and quality control 2018-09-05 https://github.com/nanakiksc/zerone 1.0 zerone 1.0 Up-to-date ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 12 14 96 0 0 0 0 0 0 0 0 0 0 0 0 96 14 12 7
CRSConverter crsconverter Tools to transforms geographical vector data to a specified coordinate reference system. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/CRSConverter 1.1 r-sf To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/CRSConverter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 3 3 https://usegalaxy.eu/published/workflow?id=89525918b2a32023 ecology/phylodiversity_workflow
EstimEndem estimate_endem Tools to estimates the endemism of each cell in a spatial grid. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/EstimEndem 0.1.1+galaxy0 r-phyloregion To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/EstimEndem 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 40 40 0 0 0 0 0 0 0 0 0 0 0 0 40 40 3 3 https://usegalaxy.eu/published/workflow?id=89525918b2a32023 ecology/phylodiversity_workflow
Geometric means (Dead wood) Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). 2023-11-10 https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60 60 163 163 0 0 0 0 0 0 0 0 2 2 20 20 183 183 62 62
MALDIquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. 2018-08-22 http://strimmerlab.org/software/maldiquant/ 1.22.0 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 31 37 985 3848 0 0 0 0 21 21 1215 1362 0 0 0 0 5210 2200 58 52 https://usegalaxy.eu/published/workflow?id=7ee6976f69131683, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://workflowhub.eu/workflows/1587?version=1 metabolomics/msi-finding-nglycans
MFAssignR mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements 2024-08-02 https://github.com/RECETOX/MFAssignR 1.1.2 r-mfassignr 1.1.2 Up-to-date Metabolomics Visualisation Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Proteomics experiment, Molecular interactions, pathways and networks, Workflows recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 80 80 2 2 13 13 0 0 0 0 0 0 0 0 93 93 7 7 https://workflowhub.eu/workflows/1351?version=1, https://workflowhub.eu/workflows/1591?version=1 metabolomics/mfassignr
Make data paper sketches from EML data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. 2024-10-15 https://github.com/TanguyGen/emldown 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 28 28 0 0 0 0 0 0 0 0 0 0 0 0 28 28 3 3
PylOccuMatcher phylogenetic_occupancy_matcher Tools to matches phylogenetic data with occupancy data. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/PhylOccuMatcher 1.0 r-phyloregion To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhylOccuMatcher 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 22 22 0 0 0 0 0 0 0 0 0 0 0 0 22 22 4 4 https://usegalaxy.eu/published/workflow?id=89525918b2a32023 ecology/phylodiversity_workflow
PyloIndex phylo_index Tools to computes the phylodiversity index. 2025-05-20 https://github.com/Morphy427/phylodiversity_workflow/PyloIndex 1.0 r-phyloregion To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhyloIndex 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 5 5 https://usegalaxy.eu/published/workflow?id=89525918b2a32023 ecology/phylodiversity_workflow
QCxMS qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). 2023-08-24 https://github.com/grimme-lab/QCxMS 5.2.1 To update Computational chemistry, Molecular Dynamics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 45445 45445 2 2 155 155 2 2 780 780 0 0 0 0 46380 46380 16 16 https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e, https://usegalaxy.eu/published/workflow?id=5465916d9b51f411, https://workflowhub.eu/workflows/1350?version=1, https://workflowhub.eu/workflows/1597?version=1, https://workflowhub.eu/workflows/897?version=3 metabolomics/qcxms-predictions
SCCAF run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. 2019-10-20 https://github.com/sccaf/sccaf 0.0.9 sccaf 0.0.10 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 8 87 110 1 1 1 1 0 0 0 0 0 0 0 0 111 88 9 7
WormsMeasurements WormsMeasurements This tool uses WoRMS (World Register of Marine Species) to add measurement values to a dataset based on scientific names. 2025-05-07 https://github.com/jeanlecras/tools-ecology 0.1.2 r-base To update Ecology ecology https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements https://github.com/galaxyecology/tools-ecology/tree/master/tools/WormsMeasurements 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 97 97 0 0 0 0 0 0 0 0 0 0 0 0 97 97 4 4 https://usegalaxy.eu/published/workflow?id=749bb05ec8674bec ecology/ecoregiolifetraits
ab1fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files 2021-10-08 1.20.0 bioconductor-sangerseqr 1.42.0 To update Convert Formats ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 65003 65003 0 0 0 0 0 0 0 0 20 20 6753 6753 71756 71756 523 523 https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 ecology/ENA_Biodiv_submission, sequence-analysis/Manage_AB1_Sanger
ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. 2019-06-13 http://ambermd.org/AmberTools.php 21.10 ambertools To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 7 2 7 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 429 458 45081 45818 158 158 1806 1806 115 115 2251 2251 0 0 0 0 49875 49138 731 702 https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=5d793801998146bc, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=84c95f31896213fd, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.eu/published/workflow?id=adc6d049e9283789, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e, https://usegalaxy.eu/published/workflow?id=e73beff62f35d677, https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab, https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=a638e12411586555, https://usegalaxy.org/published/workflow?id=aaec757e04605d3a, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://workflowhub.eu/workflows/1686?version=1, https://workflowhub.eu/workflows/247?version=2, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 computational-chemistry/htmd-analysis
analyse_short_astro_text_astro_tool analyse_short_astro_text_astro_tool Tool to analyse short astrophysics texts 2024-06-04 0.0.1+galaxy0 astroquery To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/analyse-short-astro-text 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://usegalaxy.eu/published/workflow?id=f9ae5a312e84cf0a, https://workflowhub.eu/workflows/1353?version=2
appendfdr append_fdr 2015-01-24 0.2.0 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. 2024-05-14 https://github.com/AquaINFRA/galaxy 1.0 To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 497 497 0 0 0 0 0 0 0 0 0 0 0 0 497 497 50 50
aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. 2024-10-10 https://github.com/AquaINFRA/galaxy 0.9.0 r-base To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 1826 1826 0 0 0 0 0 0 0 0 0 0 0 0 1826 1826 43 43 https://usegalaxy.eu/published/workflow?id=140b2882fc32d49f
artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis 2020-10-02 http://artbio.fr 1.10+galaxy0 samtools 1.22.1 To update SAM, Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
astronomicalarchivestool astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy 2023-07-17 0.10.21 astropy To update Data Source astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 78 78 0 0 0 0 0 0 0 0 0 0 0 0 78 78 8 8
astropytools astropy_csv2fits, astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations 2023-04-11 https://github.com/astropy/astropy 0.1.0+galaxy1 astropy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 5 5 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 5 5 https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=d9535e4afec8866b, https://usegalaxy.eu/published/workflow?id=f9ae5a312e84cf0a, https://workflowhub.eu/workflows/1267?version=1, https://workflowhub.eu/workflows/1353?version=2, https://workflowhub.eu/workflows/1369?version=1, https://workflowhub.eu/workflows/1730?version=1
atlas_fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. 2022-03-09 https://github.com/ebi-gene-expression-group/atlas-fastq-provider 0.4.4 atlas-fastq-provider 0.4.7 To update Data Source, RNA, Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bamparse bamparse Generates hit count lists from bam alignments. 2017-10-12 http://artbio.fr 4.1.1 pysam 0.23.3 To update RNA, Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baseline_toxicity_calculator tt_baseline Toxicity prediction using QSAR models 2024-03-25 https://github.com/bernt-matthias/mb-galaxy-tools 0.1.0+galaxy0 pandas To update Ecology, Text Manipulation mbernt https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations 2018-01-04 0.2.0 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 177 195 555 634 118 118 398 398 21 22 219 225 0 0 0 0 1257 1172 335 316 https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation
bgc_ocean harmonize_insitu_to_netcdf Process in-situ and biogechemical oceanographic Argo or Glider data for the Earth System 2024-12-05 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 3.0 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 75 75 0 0 0 0 0 0 0 0 0 0 0 0 75 75 5 5 https://usegalaxy.eu/published/workflow?id=44827462c065bae3, https://usegalaxy.eu/published/workflow?id=d3d9d1f173fd7bfe, https://workflowhub.eu/workflows/1961?version=1 climate/ocean_qcv_analysis
bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format 2021-10-06 http://artbio.fr 377+galaxy1 ucsc-bigwigtobedgraph 482 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 715 873 7732 9584 1 1 1 1 1 2 4 7 0 0 0 0 9592 7737 876 717
bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format 2018-09-25 https://artbio.fr 3+galaxy0 ucsc-bigwiginfo 482 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. 2018-10-03 http://thegrantlab.org/bio3d/index.php 2.4_1 r-bio3d 2.3_3 To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 5 4 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 368 408 12210 13386 109 109 1423 1423 119 122 3385 3449 0 0 0 0 18258 17018 639 596 https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=9858fdf13a522ea8, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org.au/published/workflow?id=c2f25a1bf07e8ab1, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/1697?version=1 computational-chemistry/analysis-md-simulations, computational-chemistry/htmd-analysis
biobb_pytorch biobb_pytorch_apply_mdae, biobb_pytorch_train_mdae biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library. 2024-06-26 https://github.com/bioexcel/biobb_pytorch 4.2.1 biobb_pytorch 5.1.0 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bioconductor-msnbase bioconductor_msnbase_centroid, bioconductor_msnbase_smooth_chromatogram, bioconductor_msnbase_smooth_mz MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. 2025-01-22 https://bioconductor.org/packages/release/bioc/html/MSnbase.html 2.32.0 bioconductor-msnbase 2.32.0 Up-to-date Metabolomics, Proteomics Data handling, Visualisation Data handling, Visualisation Proteomics, Proteomics experiment, Data management, Data visualisation Proteomics, Proteomics experiment, Data visualisation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase msnbase MSnbase Basic plotting, data manipulation and processing of MS-based Proteomics data. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bioconductor_mzr bioconductor_mzr_convert Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows. 2025-06-19 https://bioconductor.org/packages/mzR 2.40.0 bioconductor-mzr 2.40.0 Up-to-date Proteomics, Metabolomics Formatting Formatting Proteomics, Proteomics experiment, Data management Proteomics, Proteomics experiment recetox https://github.com/RECETOX/galaxytools/tree/main/tools/bioconductor-mzR https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-mzR mzr mzR Provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bioconductor_scp bioconductor_scp scp is a package for the single cell proteomics data processing. 2025-01-21 https://uclouvain-cbio.github.io/scp/index.html 1.16.0 bioconductor-scp 1.16.0 Up-to-date Proteomics, Single Cell Visualisation, Expression analysis Visualisation, Expression analysis Proteomics experiment, Proteomics Proteomics experiment, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp scp scp Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 4 0 0 0 0 1 1 88 88 0 0 0 0 92 92 3 3 proteomics/bioconductor-scp
biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis 2020-01-30 https://github.com/moldyn/ 1.5.2 scipy To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 98 99 539 600 119 119 638 638 0 0 0 0 0 0 0 0 1238 1177 218 217 https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://workflowhub.eu/workflows/249?version=4
biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. 2020-08-26 https://bitbucket.org/djoumbou/biotransformerjar/src/master/ 3.0.20230403 biotransformer 3.0.20230403 Up-to-date Metabolomics Metabolic pathway prediction, PTM site prediction, Natural product identification Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 1 1 92 92 1 1 2 2 95 95 3 3
blast2go blast2go Maps BLAST results to GO annotation terms 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe To update Ontology Manipulation, Sequence Analysis Gene functional annotation Gene functional annotation Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Blast2GO Blast2GO Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 205 303 851 1255 0 0 0 0 0 0 0 0 0 1 0 10 1265 851 304 205 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a
blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option 2015-01-24 https://blast.ncbi.nlm.nih.gov/ 2.6.0 blast 2.17.0 To update Sequence Analysis galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files 2014-05-15 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Gene functional annotation, Nucleic acid sequence analysis Gene functional annotation, Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh blast_rbh blast_rbh This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 413 502 25833 37031 0 0 0 0 0 0 0 0 0 0 0 0 37031 25833 502 413 https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a
blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs 2016-01-05 http://artbio.fr 1.1.0 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 8 0 0 0 0 0 0 0 0 8 0 1 0
blast_unmatched blast_unmatched Extract unmatched query sequences from blast 2017-10-03 http://artbio.fr 1.0.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits 2017-10-15 http://artbio.fr 2.7.1 python To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 8 0 0 0 0 0 0 0 0 8 0 1 0
blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs 2015-06-17 http://artbio.fr 1.1.1 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python To update Convert Formats, Sequence Analysis, Text Manipulation Sequence alignment, Sequence annotation Sequence alignment, Sequence annotation Sequence analysis Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr blastxml_to_top_descr blastxml_to_top_descr This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 530 653 263613 265902 0 0 0 0 0 0 0 0 0 0 0 0 265902 263613 653 530 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4
bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch 2015-08-28 http://proteowizard.sourceforge.net/ 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 14 22 158 1474 0 0 0 0 0 0 0 0 0 0 0 0 1474 158 22 14
c3s c3s Copernicus Climate Change Service (C3S) 2021-04-13 https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset 0.3.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17 17 422 422 7 7 10 10 3 3 139 139 0 0 0 0 571 571 27 27 https://usegalaxy.eu/published/workflow?id=21363a774a7575f0, https://usegalaxy.eu/published/workflow?id=ac5b66c42681e7a8, https://usegalaxy.eu/published/workflow?id=b610849d70c1e225, https://usegalaxy.eu/published/workflow?id=ddb21f7793eff83d, https://workflowhub.eu/workflows/1625?version=1 climate/earth_system, contributing/create-new-tutorial
cads cads Copernicus Atmosphere Data Store (ADS) 2021-06-19 https://ads.atmosphere.copernicus.eu/#!/home 0.1.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 52 52 0 0 0 0 0 0 0 0 0 0 0 0 52 52 1 1
calisp calisp Calgary approach to isotopes in proteomics 2023-06-01 https://github.com/kinestetika/Calisp/ 3.0.13 calisp 3.1.4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 507 507 0 0 0 0 0 0 0 0 0 0 0 0 507 507 4 4
cap3 cap3 cap3 wrapper 2017-09-02 http://artbio.fr 2.0.1 cap3 10.2011 To update Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 301 301 12523 12523 0 0 0 0 173 173 7922 7922 0 0 0 0 20445 20445 474 474 https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33
cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_group_comparison, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets 2018-10-01 http://cardinalmsi.org 3.4.3 bioconductor-cardinal 3.8.0 To update Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 0 9 12 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 11 9 0 156 193 30686 51576 1 1 12 12 67 69 8886 9794 26 26 132 132 61514 39716 289 250 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=785433e42d82be65, https://usegalaxy.eu/published/workflow?id=7ee6976f69131683, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.eu/published/workflow?id=fb233e418d015649, https://usegalaxy.org.au/published/workflow?id=04f6ad62f34313ea, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://usegalaxy.org.au/published/workflow?id=80cf8be8c8bf384a, https://workflowhub.eu/workflows/1455?version=1, https://workflowhub.eu/workflows/1587?version=1, https://workflowhub.eu/workflows/1593?version=1 metabolomics/msi-analyte-distribution, metabolomics/msi-finding-nglycans, proteomics/mass-spectrometry-imaging-loading-exploring-data
cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. 2021-09-01 https://code.mpimet.mpg.de/projects/cdo/ 2.0.0 To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14 14 228 228 0 0 0 0 0 0 0 0 0 0 0 0 228 228 14 14 https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3, https://workflowhub.eu/workflows/1652?version=1 ecology/x-array-map-plot
cds_essential_variability cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability 2019-05-03 https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview 0.2.0 python To update Climate Analysis, Data Source climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 45 126 355 0 0 0 0 0 0 0 0 0 0 0 0 355 126 45 33 https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612, https://workflowhub.eu/workflows/1441?version=1 climate/climate-101
cesm cesm Community Earth System Model (CESM) 2021-06-15 https://www.cesm.ucar.edu/ 2.1.3 cesm 2.1.3 Up-to-date Climate Analysis climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 14 14 0 0 0 0 0 0 0 0 0 0 0 0 14 14 2 2 https://usegalaxy.eu/published/workflow?id=46b4ad3ce0b7bc0b
champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields 2022-10-28 0.0.0 r-base To update Ecology ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 9 9 216 216 0 0 0 0 0 0 0 0 2 2 11 11 227 227 11 11 https://usegalaxy.eu/published/workflow?id=a3ad27817f77061b, https://workflowhub.eu/workflows/1690?version=1, https://workflowhub.eu/workflows/661?version=1 ecology/champs-blocs
checkv checkv_end_to_end Assess quality of single-contig viral genomes 2024-09-13 https://bitbucket.org/berkeleylab/checkv/ 1.0.3 checkv 1.0.3 Up-to-date Metagenomics Sequence assembly, Validation, Read mapping Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 4527 4527 1 1 21 21 0 0 0 0 0 0 0 0 4548 4548 84 84 https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95
cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content 2015-06-17 http://artbio.fr 4.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
climate_stripes climate_stripes Create climate stripes from a tabular input file 2019-10-05 https://www.climate-lab-book.ac.uk/2018/warming-stripes/ 1.0.2 python To update Climate Analysis, Visualization climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 31 40 183 278 5 5 22 22 3 3 276 276 0 0 0 0 576 481 48 39 https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://workflowhub.eu/workflows/123?version=1, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1441?version=1 climate/climate-101, climate/pangeo
cnv_facets facets_analysis, snp_pileup_for_facets A suite of tools for FACETS allele-specific copy number analysis. 2025-10-01 https://artbio.fr 0.6.2 snp-pileup 0.6.2 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/facets https://github.com/ARTbio/tools-artbio/tree/main/tools/facets 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
concatenate_multiple_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. 2018-03-11 http://artbio.fr 1.4.3 To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 995 996 11863 11865 511 512 3329 3331 246 332 2968 4431 1 1 3 3 19630 18163 1841 1753 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=03ef267ff7634a4b, https://usegalaxy.eu/published/workflow?id=18af9bbae833f8fe, https://usegalaxy.eu/published/workflow?id=373d861ef4b0081a, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=6aaf2b342d57f78d, https://usegalaxy.eu/published/workflow?id=7bda7ae31c427347, https://usegalaxy.eu/published/workflow?id=7cbda24fd0767899, https://usegalaxy.eu/published/workflow?id=82879b0eb4a71ad0, https://usegalaxy.eu/published/workflow?id=841367f185aaade4, https://usegalaxy.eu/published/workflow?id=8c6371b360217f72, https://usegalaxy.eu/published/workflow?id=b6457cb04bf31613, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.eu/published/workflow?id=e8a8c0b59ba9d593, https://usegalaxy.eu/published/workflow?id=ea3b120f105434ec, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=b3e775ac106e90a6, https://usegalaxy.org/published/workflow?id=2a4823c060dd216e, https://usegalaxy.org/published/workflow?id=31186e478383465b, https://usegalaxy.org/published/workflow?id=3511da8b41b1fb5d, https://usegalaxy.org/published/workflow?id=412da1489d6aed45, https://usegalaxy.org/published/workflow?id=46207bf9ce5ee26a, https://usegalaxy.org/published/workflow?id=4680511d4daad5d7, https://usegalaxy.org/published/workflow?id=4c996921fb6a2334, https://usegalaxy.org/published/workflow?id=696b2efc589afd6f, https://usegalaxy.org/published/workflow?id=7454015793c4adc9, https://usegalaxy.org/published/workflow?id=8b4945a0fb49e03e, https://usegalaxy.org/published/workflow?id=a97c694b3298ae44, https://usegalaxy.org/published/workflow?id=ac3755c1ae5f7f16, https://usegalaxy.org/published/workflow?id=af85a2ae187409f4, https://usegalaxy.org/published/workflow?id=b7c67632a6eabda5, https://usegalaxy.org/published/workflow?id=c7693951c6215e19, https://usegalaxy.org/published/workflow?id=d1ca40dd7e591025, https://usegalaxy.org/published/workflow?id=d485bf21a5069fe4, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/622?version=11 proteomics/proteogenomics-dbcreation
consalign aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences 2023-04-11 1.0.0 r-bioseq To update Sequence Analysis ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 283 283 2617 2617 0 0 0 0 0 0 0 0 16 16 4351 4351 6968 6968 299 299 https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 sequence-analysis/Manage_AB1_Sanger
consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment 2015-11-05 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab 2017-07-27 https://github.com/open2c/cooler 0.9.3 htslib 1.22.1 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 32 32 475 475 40 40 276 276 0 0 0 0 0 0 0 0 751 751 72 72 https://usegalaxy.eu/published/workflow?id=1214523f54a999fc, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=ceb0a029c6d33ec6, https://usegalaxy.eu/published/workflow?id=d9fc0df2a159e542, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.eu/published/workflow?id=fc4e3479d86f9a26, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=1e4eb6ccb47d9fc7, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=a93eb877596ce0ef, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=c8a92318855d85a5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f21d576695f9fe77, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/420?version=3
cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts 2018-07-11 http://artbio.fr 0.6.0 r-optparse 1.3.2 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
crbeam_astro_tool crbeam_astro_tool CRbeam 2024-01-31 0.0.2+galaxy0 crbeam To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/crbeam 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://workflowhub.eu/workflows/1369?version=1
cta_astro_tool cta_astro_tool Basic simulation of CTA telescope observations using gammapy package 2024-04-19 0.0.1+galaxy0 unzip To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1
ctsm_fates ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model 2020-10-21 https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api 2.0 fates-emerald To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 71 71 275 275 12 12 35 35 1 1 150 150 0 0 0 0 460 460 84 84 https://usegalaxy.eu/published/workflow?id=7b50e72deb46c6e8, https://workflowhub.eu/workflows/1427?version=1 climate/fates
custom_pro_db custom_pro_db CustomProDB 2017-10-06 https://bioconductor.org/packages/release/bioc/html/customProDB.html 1.22.0 bioconductor-rgalaxy 1.37.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 208 1876 1998 88 88 493 493 23 23 530 530 1 1 1 1 3022 2900 320 308 https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation
custom_pro_db_annotation_data_manager CustomProDB Annotation 2017-10-06 https://bioconductor.org/packages/release/bioc/html/customProDB.html To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools 2021-06-23 0.0.0 r-tangles To update Ecology ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 122 122 1286 1286 0 0 0 0 0 0 0 0 6 6 44 44 1330 1330 128 128 https://usegalaxy.eu/published/workflow?id=7b576a562031ff7e, https://usegalaxy.eu/published/workflow?id=a0404f6291874c01, https://workflowhub.eu/workflows/1693?version=1, https://workflowhub.eu/workflows/656?version=1 ecology/biodiversity-data-exploration
data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper 2019-11-11 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper 2019-11-11 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dbbuilder dbbuilder Protein Database Downloader 2015-01-24 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 997 1171 6303 7599 38 38 180 180 104 109 1413 1423 12 13 25 27 9229 7921 1331 1151 https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1464?version=1 microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/database-handling
decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. 2015-01-24 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
deseq2_normalization deseq2_normalization Normalizes gene hitlists 2018-01-05 http://artbio.fr 1.40.2+galaxy1 bioconductor-deseq2 1.46.0 To update Transcriptomics, Statistics, Single Cell artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
desi_legacy_survey_astro_tool desi_legacy_survey_astro_tool Tool to query Legacy Survey data 2024-11-14 0.0.2+galaxy0 astropy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/desi-legacy-survey 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 8 8 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=f9ae5a312e84cf0a, https://workflowhub.eu/workflows/1353?version=2, https://workflowhub.eu/workflows/1730?version=1
dfast dfast Prokaryotic genome annotation 2025-04-16 https://github.com/nigyta/dfast_core/ 1.3.6 dfast 1.3.7 To update Genome annotation Genome annotation Genome annotation Nucleic acid structure analysis, Genomics, Sequence analysis Nucleic acid structure analysis, Genomics, Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/dfast/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfast dfast DFAST Flexible prokaryotic genome annotation pipeline for faster genome publication. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dfpl dfpl_predict, dfpl_train Galaxy wrapper for deepFPlearn. 2024-12-18 https://github.com/yigbt/deepFPlearn 2.1 deepfplearn 2.1 Up-to-date Computational chemistry, Machine Learning ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfpl https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfpl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics 2015-08-26 http://diaumpire.sourceforge.net/ 2.1.3 dia_umpire 2.1.6 To update Proteomics galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 4 7 33 0 0 0 0 5 5 177 187 0 0 0 0 220 184 9 7
dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. 2020-12-23 https://github.com/shubham1637/DIAlignR 1.2.0 bioconductor-dialignr 2.10.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 40 40 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2
diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. 2023-06-26 https://github.com/vdemichev/DiaNN 1.8.1 To update Proteomics galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 31 31 181 181 0 0 0 0 29 29 333 333 0 0 0 0 514 514 60 60
diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data 2020-02-27 https://pypi.org/project/diapysef/ 0.3.5.0 diapysef 1.0.10 To update Proteomics galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 49 175 284 0 0 0 0 6 6 391 391 0 0 0 0 675 566 55 53 https://workflowhub.eu/workflows/1421?version=1 proteomics/DIA_lib_OSW
diffacto diffacto Diffacto comparative protein abundance estimation 2021-06-20 https://github.com/statisticalbiotechnology/diffacto 1.0.6 diffacto 1.0.7 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 9 9
digestdb digestdb 2015-01-24 0.1.0 trans_proteomic_pipeline To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
directag_and_tagrecon 2015-01-24 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dose_response_analysis_tool dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses 2024-04-06 https://github.com/bernt-matthias/mb-galaxy-tools 3.0.1 r-drc 3.0_1 To update Ecology ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
droplet_barcode_plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 1.6.1+galaxy2 scxa-plots 0.0.1 To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 236 247 1326 1440 88 89 379 383 3 3 51 51 1 1 4 4 1878 1760 340 328 https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 single-cell/scrna-case_alevin
earth landcover_subindicator Access, process, visualise oceanographic data for the Earth System 2024-10-21 https://github.com/Marie59/FE-ft-ESG/tree/main/earth 0.1.0 numpy To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1
ecoregionalization ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ClaraGuess, ecoregion_clara_cluster, ecoregion_eco_map, indicspecies, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. 2023-07-26 https://github.com/PaulineSGN/Workflow_Galaxy 0.1.2+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0 0 8 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 13 13 987 987 0 0 0 0 0 0 0 0 0 0 0 0 987 987 13 13 https://usegalaxy.eu/published/workflow?id=749bb05ec8674bec, https://usegalaxy.eu/published/workflow?id=89ff2a1143954d83, https://usegalaxy.eu/published/workflow?id=b727b64f37238fff, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1209?version=1, https://workflowhub.eu/workflows/1680?version=1, https://workflowhub.eu/workflows/658?version=1 ecology/Ecoregionalization_tutorial, ecology/ecoregiolifetraits
eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences 2019-11-11 2.1.8 eggnog-mapper 2.1.13 To update Proteomics Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 3 0 1977 2018 64994 65580 518 518 9634 9634 541 541 25986 25986 144 144 66224 66224 167424 166838 3221 3180 https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 genome-annotation/funannotate, genome-annotation/functional
embl2fa embl2fa Converts EMBL flat format to fasta format 2022-11-12 http://artbio.fr 0.2 To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
emlassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa 2023-07-21 https://github.com/EDIorg/EMLassemblyline 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 40 40 646 646 0 0 0 0 0 0 0 0 1 1 2 2 648 648 41 41 https://usegalaxy.eu/published/workflow?id=a30d511e3dda0895, https://usegalaxy.eu/published/workflow?id=ab89c61db3d7abbb
encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis 2020-09-11 https://bitbucket.org/searleb/encyclopedia/wiki/Home 1.12.34 encyclopedia 2.12.30 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 34 34 893 893 3 3 42 42 7 7 58 58 0 0 0 0 993 993 44 44 https://usegalaxy.eu/published/workflow?id=14f9c2099db30570, https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7, https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20, https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1, https://usegalaxy.eu/published/workflow?id=6d494e2f634eba70, https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9, https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b, https://usegalaxy.eu/published/workflow?id=f1309010689eb98a, https://workflowhub.eu/workflows/1471?version=1 proteomics/encyclopedia
eodie eodie Earth Observation Data Information Extractor 2021-12-30 https://eodie.readthedocs.io/ 1.0.2 eodie To update Climate Analysis climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 45 45 0 0 0 0 0 0 0 0 0 0 0 0 45 45 4 4
eukcc eukcc_single Galaxy wrapper for EukCC 2025-07-25 https://github.com/EBI-Metagenomics/EukCC 2.1.3 eukcc 2.1.3 Up-to-date Metagenomics Sequence assembly validation Sequence assembly validation Metagenomics Metagenomics ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc eukcc EukCC EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ez_histograms ez_histograms ggplot2 histograms and density plots 2024-02-07 https://github.com/tidyverse/ggplot2 3.4.4 r-ggplot2 2.2.1 To update Visualization, Statistics Data analysis, Statistical calculation, Visualisation Statistical calculation, Visualisation Ecology Ecology artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms ez_histograms ez_histograms This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together 2015-01-24 https://github.com/galaxyproteomics/tools-galaxyp/ 1.2.0 python To update Fasta Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1552 1771 35725 38519 1724 1724 42712 42712 289 306 5517 6718 32 33 400 402 88351 84354 3834 3597 https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, 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https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/1474?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1788?version=1, https://workflowhub.eu/workflows/1793?version=1, https://workflowhub.eu/workflows/1839?version=1 microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/database-handling, proteomics/neoantigen-fragpipe-discovery, proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation
fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG 2020-07-23 https://github.com/galaxyproteomics/fastg2protlib.git 1.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7 7 31 31 0 0 0 0 0 0 0 0 0 0 0 0 31 31 7 7
fastq_pair fastq_pair Paired-end fastq pairer 2022-03-17 https://github.com/linsalrob/fastq-pair 1.0+galaxy0 fastq-pair 1.0 To update Fastq Manipulation ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality 2022-03-11 https://github.com/agordon/fastx_toolkit 0.0.14+galaxy0 fastx_toolkit 0.0.14 To update Fastq Manipulation ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files 2022-02-15 https://github.com/nunofonseca/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.3 To update Transcriptomics, RNA ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy 2015-02-06 0.11.0 msproteomicstools 0.11.0 Up-to-date Proteomics galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 19 19 0 0 0 0 0 0 0 0 0 0 0 0 19 19 2 2
fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers 2015-06-17 http://artbio.fr 3.1.0 urllib3 1.12 To update Fasta Manipulation, Data Source artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 4 5 0 2 0
filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences 2015-01-24 2.3 python To update Fasta Manipulation, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 1293 1457 109310 115300 1547 1547 53560 53560 301 301 12056 12056 54 54 483 483 181399 175409 3359 3195 https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a, https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1, https://usegalaxy.eu/published/workflow?id=21fc597d983f1194, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=69e603a2da979c93, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82a60d94d699efbf, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=b51559006f86db9e, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=fba0eb562a710733, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050, https://usegalaxy.org/published/workflow?id=94da3d448bb8a137, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1717?version=2 sequence-analysis/Manage_AB1_Sanger, sequence-analysis/tapscan-streptophyte-algae, transcriptomics/mirna-target-finder
filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. 2021-01-06 https://github.com/RECETOX/galaxytools/ 3.1.1 openbabel 2.3.90dev7d621d9 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_density filterdensity Filter out position based on distance between SNVs 2015-11-19 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_stats filterstat SNVPhyl filter_stats 2015-07-31 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_vcf filtervcf SNVPhyl filter_vcf 2015-08-04 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer 2015-07-31 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fishertest fishertest Fisher's exact test on two-column hit lists. 2015-06-17 http://artbio.fr 2.32.0+galaxy0 bioconductor-qvalue 2.38.0 To update RNA, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fits2tiff_astro_tool fits2tiff_astro_tool Tool to convert FITS files to TIFF 2025-07-18 0.0.1+galaxy0 astropy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/fits2tiff 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 4 4 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1
flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification 2017-12-06 https://github.com/smith-chem-wisc/FlashLFQ 1.0.3.1 flashlfq 2.1.4 To update Proteomics Label-free quantification Label-free quantification Proteomics experiment, Proteomics Proteomics experiment, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 59 516 760 0 0 0 0 16 16 216 226 0 0 0 0 986 732 75 63 https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://workflowhub.eu/workflows/1450?version=1 proteomics/metaquantome-data-creation
fragpipe fragpipe, fragpipe_manifest_generator Data analysis for mass spectrometry-based proteomics. 2022-07-21 https://fragpipe.nesvilab.org/ 23.0 fragpipe 23.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 41 435 435 23 23 70 70 0 0 0 0 0 0 0 0 505 505 64 64 https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1793?version=1 proteomics/neoantigen-fragpipe-discovery
freeenergy Free energy tools of BRIDGE. 2019-10-24 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
freqsap freqsap Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP. 2025-07-18 https://github.com/RECETOX/galaxytools 1.0.0+galaxy0 pandas To update Proteomics recetox https://github.com/RECETOX/galaxytools/tree/main/tools/freqsap https://github.com/RECETOX/galaxytools/tree/master/tools/freqsap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis 2021-08-16 http://frogs.toulouse.inrae.fr/ 4.2.0 frogs 5.0.2 To update Metagenomics frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 0 0 0 28 0 0 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1271 1272 73623 73661 73661 73623 1272 1271 https://usegalaxy.fr/published/workflow?id=048cb90ec1ac7120, https://usegalaxy.fr/published/workflow?id=2ac84b2bd45876cf, https://usegalaxy.fr/published/workflow?id=b46954345641a3b8, https://usegalaxy.fr/published/workflow?id=d68b4aa5337f016b
from_hicup_to_juicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. 2018-06-05 0.0.2 pysam 0.23.3 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fromgtftobed12 fromgtfTobed12 Convert GTF files to BED12 format 2019-07-31 https://pythonhosted.org/gffutils/contents.html 0.11.1+galaxy1 gffutils 0.13 To update Convert Formats lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations 2021-12-29 http://artbio.fr 4.1.7.0 gatk4 4.6.2.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gc_derivatization gc_derivatization In silico derivatization for GC. 2024-03-15 https://github.com/RECETOX/gc-meox-tms 1.0.1 gc-meox-tms 1.0.1 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 6 6 0 0 0 0 1 1 45 45 0 0 0 0 51 51 3 3
gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. 2019-02-25 https://www.gdal.org 3.0.0 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 11 15 724 1525 0 0 0 0 0 0 0 0 2 2 3 3 1528 727 17 13 https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/1670?version=1, https://workflowhub.eu/workflows/404?version=1 ecology/gbif_cleaning
genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences 2024-06-17 https://github.com/apcamargo/genomad/ 1.11.1 genomad 1.11.1 Up-to-date Metagenomics Sequence annotation, Taxonomic classification Sequence annotation, Taxonomic classification Sequence analysis Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 119 119 2576 2576 20 20 71 71 0 0 0 0 0 0 0 0 2647 2647 139 139 https://usegalaxy.eu/published/workflow?id=36de05d50c703164
get_reference_fasta get_fasta_reference Obtain reference genome sequence. 2015-06-17 http://artbio.fr 0.3.2 To update Data Source, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gettn5extendedcoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension 2018-06-13 0.0.2 pysam 0.23.3 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED 2018-01-10 https://github.com/gpertea/gffcompare/ 0.2.1 python To update Convert Formats galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 381 435 1352 2561 460 460 1295 1295 79 81 657 677 0 0 0 0 4533 3304 976 920 https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=656ebad61341f89f, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation
grb_detection_astro_tool grb_detection_astro_tool SPI-ACS GRB detection 2025-08-13 0.0.1+galaxy0 numpy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/grb-detection 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. 2018-10-03 https://github.com/gromacs 2022 gromacs 2021.3 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 14 8 15 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 800 895 211260 221677 520 520 42336 42336 171 177 13561 13803 0 0 0 0 277816 267157 1592 1491 https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=5d793801998146bc, https://usegalaxy.eu/published/workflow?id=7969bdac8adb8810, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=84c95f31896213fd, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.eu/published/workflow?id=ac84daeb82d76e1c, https://usegalaxy.eu/published/workflow?id=adc6d049e9283789, https://usegalaxy.eu/published/workflow?id=b51b2f4950d26b07, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://usegalaxy.eu/published/workflow?id=d873ff816f028d4f, https://usegalaxy.eu/published/workflow?id=d91e715b5e3457d3, https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.eu/published/workflow?id=e73beff62f35d677, https://usegalaxy.eu/published/workflow?id=fb425d6accf3ca55, https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org.au/published/workflow?id=8a20b3ed4a81263d, https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://usegalaxy.org/published/workflow?id=a638e12411586555, https://usegalaxy.org/published/workflow?id=aaec757e04605d3a, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://usegalaxy.org/published/workflow?id=d2b994833b79d2cb, https://workflowhub.eu/workflows/1645?version=1, https://workflowhub.eu/workflows/1686?version=1, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/247?version=2, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/249?version=4, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 computational-chemistry/htmd-analysis, computational-chemistry/md-simulation-gromacs
gsc_center_scale center_scale Center or scale (standardize) data 2019-07-09 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Statistics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_filter_cells filter_cells Filter single cell RNAseq data on library depth and number of detected genes 2019-06-23 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data 2019-06-23 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations 2019-06-24 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation 2019-06-23 http://artbio.fr 4.3+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Visualization, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data 2019-06-23 http://artbio.fr 4.1.3+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_scran_normalize scran_normalize Normalize raw counts using scran 2019-09-23 http://artbio.fr 1.28.1+galaxy1 bioconductor-scran 1.34.0 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 125 125 18 18 334 334 5 5 157 157 0 0 0 0 616 616 57 57
gsc_signature_score signature_score Compute signature scores from single cell RNAseq data 2019-06-23 http://artbio.fr 2.3.9+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gtf2gene_list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 429 449 2337 2550 463 464 1318 1322 52 52 292 292 2 2 5 5 4169 3952 967 946 https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b, https://usegalaxy.eu/published/workflow?id=73b41b975da284d5, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=aeb0f5b74e51f5c2, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 single-cell/scrna-case_alevin
guppy_basecaller guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr 6.5.7+galaxy0 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 0 0 0 0 7 7 1 1
hardklor hardklor, kronik Hardklör 2016-04-26 2.30.1+galaxy1 hardklor 2.3.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3 6 25 111 0 0 0 0 0 0 0 0 0 0 0 0 111 25 6 3
hess_astro_tool hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope 2024-02-19 0.0.2+galaxy0 ipython To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 8 8 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 https://workflowhub.eu/workflows/766?version=1
high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps 2019-07-20 https://github.com/cran/gplots 3.1.3+galaxy0 r-gplots 2.17.0 To update Visualization artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hirieftools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools 2017-04-11 1.3 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. 2024-06-07 https://github.com/AquaINFRA/galaxy 0.2.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 237 237 0 0 0 0 0 0 0 0 0 0 0 0 237 237 4 4 https://usegalaxy.eu/published/workflow?id=6173008772bdba09, https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704
hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack 2023-02-27 20241220 Fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX 2019-02-22 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 34 55 278 0 0 0 0 0 0 0 0 0 0 0 0 278 55 34 12
iedb_netmhcpan iedb_netmhciipan, iedb_netmhcpan Predict binding of peptides to any MHC or MHC II molecule of known sequence using artificial neural networks 2025-07-09 http://tools.immuneepitope.org/main/tools-api/ 4.1+galaxy0 To update Data Source, Sequence Analysis galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 19 19 0 0 0 0 0 0 0 0 0 0 0 0 19 19 2 2
incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server 2023-02-17 20231221 Fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file 2024-01-05 https://github.com/AquaINFRA/galaxy 1.0 r-getopt To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 70 70 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://workflowhub.eu/workflows/807?version=1
ipaPy2 ipapy2_MS1_annotation, ipapy2_MS2_annotation, ipapy2_clustering, ipapy2_compute_all_adducts, ipapy2_compute_bio, ipapy2_gibbs_sampler, ipapy2_gibbs_sampler_add, ipapy2_map_isotope_patterns Mass spectrometry data annotation tool. 2023-12-04 https://github.com/francescodc87/ipaPy2 1.3.0 ipapy2 1.3.0 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
iphop iphop_predict Integrated Phage Host Prediction 2024-10-14 https://bitbucket.org/srouxjgi/iphop/ 1.3.3 iphop 1.4.1 To update Metagenomics Sample comparison Sample comparison ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 26 26 0 0 0 0 0 0 0 0 0 0 0 0 26 26 9 9
isolib isolib Create an isotopic pattern library for given compounds and adducts. 2023-10-26 https://github.com/RECETOX/galaxytools/ 2.6+galaxy3 bioconductor-metabocoreutils 1.14.0 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 6 6 0 0 0 0 1 1 219 219 0 0 0 0 225 225 3 3
justdiff justdiff Unix diff 2017-09-27 http://artbio.fr 3.10+galaxy0 diffutils To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
justgzip justgzip Compress fastq sequence files 2018-05-16 http://artbio.fr 2.8+galaxy0 pigz To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 20 20 20 20 1 1
lambdaminer lm_get_projects Lambda-Miner Tools 2025-03-06 https://lambda-miner-project.pages.ufz.de/lambda-miner-workflows/ 0.1.0+galaxy0 pandas To update Web Services, Data Source ufz https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/lambdaminer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation 2018-10-02 https://github.com/compomics/LFQ_galaxy_p 1.0 bioconductor-msnbase 2.32.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 19 27 117 0 0 0 0 0 0 0 0 0 0 0 0 117 27 19 9
longorf longORF obtain longest ORF in six-frame translations 2018-06-01 0.3.0 To update Sequence Analysis mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ltq_iquant_cli 2015-01-24 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow 2020-07-12 http://artbio.fr 0.2.8 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lumpy_sv lumpy Find structural variations 2017-07-24 http://artbio.fr 1.3 lumpy-sv 0.3.1 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
make_nr make_nr Make a FASTA file non-redundant 2018-11-06 https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Sequence alignment, Genome annotation Sequence alignment, Genome annotation Molecular biology, Sequence analysis Molecular biology, Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr make_nr make_nr Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
manta manta Structural variant and indel caller for mapped sequencing data 2019-10-25 http://artbio.fr 1.6 manta 1.6.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 88 88 1118 1118 0 0 0 0 0 0 0 0 0 0 0 0 1118 1118 88 88
map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser 2016-01-13 0.2 biopython 1.70 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 9 10 46 0 0 0 0 0 0 0 0 0 0 0 0 46 10 9 5
mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file 2022-06-15 http://artbio.fr 0.22.0 r-optparse 1.3.2 To update Sequence Analysis, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data 2024-07-26 https://github.com/Finn-Lab/SanntiS 0.9.3.5 sanntis 0.9.4.1 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 198 198 0 0 0 0 5 5 112 112 0 0 0 0 310 310 27 27 https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://workflowhub.eu/workflows/1663?version=1 ecology/marine_omics_bgc
matchms matchms_add_key, matchms_convert, matchms_matchms_export_skyline_transition_list, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. 2020-11-16 https://github.com/matchms/matchms 0.30.2 matchms 0.31.0 To update Metabolomics Spectral library search, Format validation, Filtering Spectral library search, Format validation, Filtering Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 28 28 1904 1904 5 5 29 29 5 5 4132 4132 27 27 399 399 6464 6464 65 65 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.eu/published/workflow?id=3358c516f5412e92, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/1582?version=1, https://workflowhub.eu/workflows/888?version=2 metabolomics/gc_ms_with_xcms
max_projections_stack_and_upload_omero max_projections_stack_and_upload_omero Combine images from max projections to stack and upload to the omero server 2024-12-12 20241213.2 Fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
maxquant maxquant, maxquant_mqpar wrapper for MaxQuant 2015-01-24 https://www.maxquant.org/ 2.0.3.0 maxquant 2.0.3.0 Up-to-date Proteomics Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability Proteomics experiment, Proteomics, Statistics and probability galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1628 1682 7932 8757 775 775 3791 3791 407 416 3720 3831 3 3 33 33 16412 15476 2876 2813 https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=96d198ed953449fd, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=2404d5e5b1817825, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1177?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1420?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1468?version=1 microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-4-quantitation, proteomics/DIA_lib_OSW, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/maxquant-msstats-tmt
md_converter md_converter A tool for interconverting between different MD structure and trajectory file formats. 2018-10-13 1.9.7 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 309 342 27397 27743 75 75 849 849 105 105 1433 1433 0 0 0 0 30025 29679 522 489 https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/248?version=4 computational-chemistry/htmd-analysis, computational-chemistry/med-chem-data, fair/med-chem-data
md_converter md_slicer A tool for slicing trajectory files using MDTraj. 2019-10-07 1.9.9 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 21 102 179 4 4 6 6 7 7 539 539 0 0 0 0 724 647 32 27
mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations 2018-10-04 https://github.com/MDAnalysis/mdanalysis 1.0.0 mdanalysis To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 10 5 10 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 164 177 2894 3569 33 33 238 238 52 52 935 935 0 0 0 0 4742 4067 262 249 https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=b47e415f80941ba0, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/1694?version=1 computational-chemistry/analysis-md-simulations, computational-chemistry/htmd-analysis
mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories 2020-06-24 https://github.com/mdtraj/mdtraj 1.9.7 mdtraj To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 36 36 4 4 63 63 0 0 0 0 0 0 0 0 99 99 12 12
mean_per_zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file 2019-03-15 https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ 0.2.0 python To update Visualization, GIS, Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 3 1 25 0 0 0 0 0 0 0 0 0 0 0 0 25 1 3 1
measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index 2022-01-18 20221216 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa 2023-11-30 https://github.com/jeremyfix/medenv 0.1.0 pandas To update Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 38 38 0 0 0 0 0 0 0 0 0 0 0 0 38 38 11 11
meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer 2017-03-03 https://github.com/compomics/meta-proteome-analyzer/ 2.0.0 mpa-portable 2.0.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22 22 148 148 0 0 0 0 0 0 0 0 0 0 0 0 148 148 22 22
metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ 1.0 metagene_annotator 1.0 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Genomics, Model organisms, Data submission, annotation and curation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 439 457 20971 21069 0 0 0 0 0 0 0 0 0 0 0 0 21069 20971 457 439 https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178
metanovo metanovo Produce targeted databases for mass spectrometry analysis. 2022-03-29 https://github.com/uct-cbio/proteomics-pipelines 1.9.4 metanovo 1.9.4 Up-to-date Proteomics Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 5000 5000 5 5 34 34 4 4 92 92 0 0 0 0 5126 5126 49 49 https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation
metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function 2018-11-27 https://github.com/galaxyproteomics/metaquantome/ 2.0.2 metaquantome 2.0.2 Up-to-date Proteomics Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 80 89 2277 3166 0 0 0 0 27 27 2323 2323 0 0 0 0 5489 4600 116 107 https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d, https://workflowhub.eu/workflows/1453?version=1, https://workflowhub.eu/workflows/1459?version=1 proteomics/metaquantome-function, proteomics/metaquantome-taxonomy
mgf_formatter mgf_formatter 2014-09-26 1.0.0 mgf-formatter 1.0.0 Up-to-date galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mircounts mircounts Generates miRNA count lists from read alignments to mirBase. 2017-06-12 http://artbio.fr 1.6 tar To update RNA, Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 30 30 44 44 1868 1868 0 0 0 0 1898 1898 45 45
misc target_screen, use_theoretical_mz_annotations 2024-02-16 https://github.com/RECETOX/galaxytools 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 151 151 0 0 0 0 1 1 90 90 0 0 0 0 241 241 5 5 https://workflowhub.eu/workflows/888?version=2
morpheus morpheus Morpheus MS Search Application 2015-10-29 https://cwenger.github.io/Morpheus 288 morpheus 290 To update Proteomics Peptide database search Peptide database search Proteomics Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10 20 77 205 0 0 0 0 157 157 1237 1273 0 0 0 0 1478 1314 177 167
mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA 2022-03-31 https://github.com/galaxyproteomics/tools-galaxyp/ 0.1.19 bioconductor-preprocesscore 1.68.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 4 4 15 15 0 0 0 0 0 0 0 0 0 0 0 0 15 15 4 4
ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. 2024-08-15 https://github.com/matchms/ms2deepscore 2.0.0 ms2deepscore 2.5.4 To update Metabolomics Spectrum calculation, Spectral library search, Network analysis Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container 2015-01-24 http://proteowizard.sourceforge.net/tools.shtml 3.0.20287 To update Proteomics Filtering, Formatting Filtering, Formatting Proteomics, Proteomics experiment Proteomics, Proteomics experiment galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 550 604 58574 66339 133 133 2254 2254 76 76 4844 4844 108 113 7765 7906 81343 73437 926 867 https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=14f9c2099db30570, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20, https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6d3332794ceca465, https://usegalaxy.eu/published/workflow?id=6d494e2f634eba70, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://usegalaxy.org.au/published/workflow?id=762791e094457bf2, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=8ecc114eb9097855, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1416?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1450?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/1471?version=1, https://workflowhub.eu/workflows/1582?version=1, https://workflowhub.eu/workflows/1791?version=1 metabolomics/gc_ms_with_xcms, microbiome/clinical-mp-2-discovery, proteomics/DIA_Analysis_OSW, proteomics/clinical-mp-2-discovery, proteomics/encyclopedia, proteomics/metaquantome-data-creation, proteomics/neoantigen-peptide-verification, proteomics/protein-id-oms
msgfplus msgfplus MSGF+ 2015-11-10 0.5 msgf_plus 2024.03.26 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 54 762 944 0 0 0 0 0 0 0 0 0 0 0 0 944 762 54 34
msmetaenhancer msmetaenhancer 2021-11-22 https://github.com/RECETOX/MSMetaEnhancer 0.4.1 msmetaenhancer 0.4.1 Up-to-date Metabolomics Annotation, Standardisation and normalisation Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Metabolomics, Compound libraries and screening, Data submission, annotation and curation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 241 241 0 0 0 0 2 2 112 112 3 3 13 13 366 366 17 17 https://workflowhub.eu/workflows/888?version=2
msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. 2019-10-23 1.0.0 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7 12 21 113 0 0 0 0 0 0 0 0 0 1 0 8 121 21 13 7 https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=c750484145c9903b
msp_merge msp_merge 2022-05-05 https://github.com/RECETOX/galaxytools 0.1.0 matchms 0.31.0 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
msstatstmt msstats MSstats tool for analyzing mass spectrometry proteomic datasets 2020-07-25 https://github.com/MeenaChoi/MSstats 4.0.0 bioconductor-msstats 4.14.0 To update Proteomics Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression Proteomics, Proteomics experiment, Protein expression galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 800 803 2969 3004 283 283 1456 1456 99 99 1605 1605 0 0 0 0 6065 6030 1185 1182 https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://workflowhub.eu/workflows/1426?version=1, https://workflowhub.eu/workflows/1458?version=1, https://workflowhub.eu/workflows/1462?version=1 proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq
msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 2021-01-20 http://msstats.org/msstatstmt/ 2.0.0 bioconductor-msstatstmt 2.10.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 113 113 844 844 10 10 47 47 18 18 693 693 0 0 0 0 1584 1584 141 141 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1482?version=1 microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/maxquant-msstats-tmt
mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome 2020-06-23 1.1.0 r-tidyverse To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 43 258 286 0 0 0 0 0 0 0 0 0 0 0 0 286 258 43 39
mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs 2020-09-13 http://artbio.fr 3.12.0 bioconductor-mutationalpatterns 3.16.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data 2015-06-01 https://github.com/galaxyproteomics/mzToSQLite 2.1.1+galaxy0 mztosqlite 2.1.1 To update Proteomics Conversion, Peptide database search Conversion, Peptide database search Proteomics, Biological databases Proteomics, Biological databases galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 136 146 868 959 17 17 83 83 18 18 336 336 0 0 0 0 1378 1287 181 171 https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://workflowhub.eu/workflows/1429?version=1 proteomics/proteogenomics-dbsearch
mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. 2023-01-12 https://github.com/RECETOX/galaxytools 0.1.0+galaxy2 lxml To update Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzspeclib mzspeclib_convert, mzspeclib_describe, mzspeclib_validate mzspeclib is a library and set of tools for handling, converting, and validating mass spectral libraries in a standardized format. This suite provides Galaxy wrappers for mzspeclib's core functionalities, including conversion and validation of spectral libraries. 2025-06-12 https://github.com/HUPO-PSI/mzspeclib-py 1.0.7 mzspeclib 1.0.7 Up-to-date Proteomics, Metabolomics Conversion, Format validation Conversion, Format validation Proteomics, Metabolomics Proteomics, Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/main/tools/mzspeclib https://github.com/RECETOX/galaxytools/tree/master/tools/mzspeclib mzspeclib mzspeclib A python reference implementation of the mzSpecLib spectral library format. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mztabm mztabm_validate Tools for handling mzTab-M files using various packages. 2025-07-01 https://github.com/lifs-tools/jmzTab-m 1.0.6 jmztab-m 1.0.6 Up-to-date Metabolomics Loading, Format validation, Formatting Format validation, Formatting Ontology and terminology, Metabolomics, Data submission, annotation and curation Ontology and terminology, Metabolomics, Data submission, annotation and curation recetox https://github.com/RECETOX/galaxytools/tree/main/tools/mztabm https://github.com/RECETOX/galaxytools/tree/master/tools/mztabm jmztab-m jmztab-m Reference implementation for mzTab 2.0 for metabolomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ 2013-09-23 https://blast.ncbi.nlm.nih.gov/ 2.16.0 blast 2.17.0 To update Sequence Analysis devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 16 16 16 16 0 0 0 0 0 0 0 0 0 0 16 16 16 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 4564 5012 608297 687163 5091 6262 690841 770815 1316 1731 262398 287817 159 164 12993 13154 1758949 1574529 13169 11130 https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, 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proteomics/proteogenomics-novel-peptide-analysis, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/ncbi-blast-against-the-madland, sequence-analysis/viral_primer_design
nfdi4earth_os4a_importer nfdi4earth_os4a A data source tool for downloading datasets via NFDI4Earth's OneStop4All search user interface. 2025-09-23 https://onestop4all.nfdi4earth.de/ 1.0 To update Ecology ecology https://git.rwth-aachen.de/nfdi4earth/onestop4all/onestop4all-implementation/-/tree/develop https://github.com/galaxyecology/tools-ecology/tree/master/tools/nfdi4earth_os4a_importer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
oases oasesoptimiserv Short read assembler 2017-10-15 http://artbio.fr 1.4.0 oases 0.2.09 To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis 2022-11-04 https://github.com/Marie59/obisindicators 0.0.2 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 399 399 15 15 25 25 0 0 0 0 0 0 0 0 424 424 44 44 https://usegalaxy.eu/published/workflow?id=4f51080ffe7d57e0, https://usegalaxy.eu/published/workflow?id=9e05bd65faf58ab3, https://workflowhub.eu/workflows/1698?version=1, https://workflowhub.eu/workflows/662?version=1, https://workflowhub.eu/workflows/758?version=1 climate/earth_system, ecology/obisindicators
ocean argo_getdata, copernicusmarine, divand_full_analysis Access, process, and visualise oceanographic data for the Earth System 2023-11-17 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 0.1.15 copernicusmarine To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 189 189 0 0 0 0 0 0 0 0 0 0 0 0 189 189 14 14 https://usegalaxy.eu/published/workflow?id=26fe6b0fb6ca2892, https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892, https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7, https://workflowhub.eu/workflows/1436?version=1, https://workflowhub.eu/workflows/1445?version=1 climate/argo_pangeo, climate/earth_system, climate/ocean-variables
ocean_data_view_manager tool_biogeochemical_calibration, tool_odv, tool_odv_history The tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet in an automatic way. 2025-03-18 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 2.1 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 112 112 0 0 0 0 0 0 0 0 0 0 0 0 112 112 4 4 https://usegalaxy.eu/published/workflow?id=44827462c065bae3, https://usegalaxy.eu/published/workflow?id=d3d9d1f173fd7bfe, https://workflowhub.eu/workflows/1961?version=1 climate/ocean_qcv_analysis
ocean_neural_network bgc_canyon_b Robust Estimation of Open Ocean CO2 Variables and Nutrient Concentrations From T, S, and O2 Data Using Bayesian Neural Networks 2025-03-18 https://github.com/Marie59/FE-ft-ESG/tree/main/ocean 0.9.3 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_neural_network https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_neural_network 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. 2024-03-12 https://github.com/AquaINFRA/galaxy 1.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 100 100 0 0 0 0 0 0 0 0 0 0 0 0 100 100 8 8 https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704, https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470
ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. 2024-03-12 https://github.com/AquaINFRA/galaxy 1.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 57 57 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470
omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down 2023-06-23 20230623 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id 2023-12-22 0.2.0 omero-py 5.11.1 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_get_full_images omero_get_full_images Get full images from omero 2024-05-21 20240521 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels 2023-03-24 20230809 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements 2023-03-24 20240214 fiji 20250206 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_upload omero_dataset_to_plate, omero_filter, omero_get_id, omero_get_value, omero_import, omero_metadata_import, omero_roi_import Interact with an OMERO.server using omero-py and ezomero. 2024-02-07 https://github.com/ome/omero-py/ 5.18.0 To update Imaging Image analysis Image analysis Imaging, Data visualisation Imaging, Data visualisation ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 4 0 0 0 0 0 0 0 0 0 0 0 0 4 4 2 2 https://workflowhub.eu/workflows/1258?version=1, https://workflowhub.eu/workflows/1259?version=1 imaging/omero-suite
openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. 2022-03-25 https://github.com/openmm 1.8.1 pdbfixer To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 100 100 1933 1933 0 0 0 0 0 0 0 0 0 0 0 0 1933 1933 100 100
openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses 2017-02-21 https://www.openms.de/ 3.1 openms 3.4.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 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https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1424?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1446?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1452?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/613?version=2 proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil
packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations 2018-10-04 http://m3g.iqm.unicamp.br/packmol/home.shtml 18.169.1 packmol To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30 36 208 300 12 12 434 434 0 0 0 0 0 0 0 0 734 642 48 42
pampa pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics 2020-06-06 0.0.2 To update Ecology ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 50 53 1997 2045 0 0 0 0 26 26 1141 1141 1 1 1 1 3187 3139 80 77 https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f, https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c, https://workflowhub.eu/workflows/1696?version=1 ecology/PAMPA-toolsuite-tutorial
pathifier pathifier pathifier 2019-09-03 https:// 1.40.0 bioconductor-pathifier 1.44.0 To update Transcriptomics, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 13 13 265 265 0 0 0 0 0 0 0 0 0 0 0 0 265 265 13 13
pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. 2017-12-19 0.1.3+galaxy1 python To update Genomic Interval Operations, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 73 78 603 666 16 16 27 27 12 12 215 215 0 0 0 0 908 845 106 101 https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d, https://usegalaxy.eu/published/workflow?id=4bd0827030df02a3, https://usegalaxy.eu/published/workflow?id=d375fb9af8d46793, https://usegalaxy.eu/published/workflow?id=f946efa49bd41a43, https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e, https://usegalaxy.org.au/published/workflow?id=cf5ab8fe4e2c0859, https://usegalaxy.org/published/workflow?id=336d74481d2f721a, https://workflowhub.eu/workflows/1457?version=1, https://workflowhub.eu/workflows/1467?version=1, https://workflowhub.eu/workflows/1790?version=1 proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-novel-peptide-analysis
pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. 2020-01-22 https://pepquery.org 1.6.2 pepquery 2.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 75 77 7231 7437 0 0 0 0 0 0 0 0 0 0 0 0 7437 7231 77 75 https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=470b629d22b0fc51, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6201ec86d380aef1, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6da171871d4f3fd5, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=79eb28066236e836, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8bb3bc745ea62bed, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a372f693471beb56, https://usegalaxy.eu/published/workflow?id=adf5e8bead686341, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e, https://usegalaxy.eu/published/workflow?id=c02ff9e97ce796c6, https://usegalaxy.eu/published/workflow?id=ca342c5018c210e7, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d95a3349f38792fc, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289
pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation 2022-10-02 https://pepquery.org 2.0.2 pepquery 2.0.2 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 3 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 34 34 5598 5598 5 5 67 67 8 8 251 251 0 0 0 0 5916 5916 47 47 https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=6d3332794ceca465, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=8e997deae5a382c4, https://usegalaxy.eu/published/workflow?id=9b4e6c5f2c1babce, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.org.au/published/workflow?id=762791e094457bf2, https://usegalaxy.org.au/published/workflow?id=832a30759469d3fe, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=8ecc114eb9097855, https://usegalaxy.org/published/workflow?id=d0847ce8261eb922, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1406?version=1, https://workflowhub.eu/workflows/1416?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/1789?version=1, https://workflowhub.eu/workflows/1791?version=1 microbiome/clinical-mp-3-verification, proteomics/clinical-mp-3-verification, proteomics/neoantigen-hla-binding-novel-peptides, proteomics/neoantigen-peptide-verification
peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files 2019-03-29 1.0.0 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 72 76 520 566 11 11 17 17 8 8 199 199 0 0 0 0 782 736 95 91 https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d, https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e, https://workflowhub.eu/workflows/1467?version=1 proteomics/proteogenomics-novel-peptide-analysis
peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI 2015-01-31 http://compomics.github.io searchgui 4.3.15 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 541 635 10278 19384 236 236 1790 1790 54 54 3790 3855 2 3 15 21 25050 15873 928 833 https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=249c7569b61fb349, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6aca8a72626c521b, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6bd8311554412c38, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9c0132dd81297afe, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d1d5a6bd6571d47f, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f34c76e2d8045725, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1429?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1443?version=1, https://workflowhub.eu/workflows/1450?version=1 microbiome/clinical-mp-2-discovery, proteomics/clinical-mp-2-discovery, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/protein-id-sg-ps, proteomics/proteogenomics-dbsearch
pepxml_to_xls Convert PepXML to Tabular 2015-01-24 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator 2016-04-12 3.5 percolator 3.7.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 6 7 58 378 0 0 0 0 4 4 1434 1454 0 0 0 0 1832 1492 11 10
phabox phabox_cherry, phabox_contamination, phabox_end_to_end, phabox_phagcn, phabox_phamer, phabox_phatyp, phabox_phavip, phabox_tree, phabox_votu Identify and analyze phage contigs in metagenomic data 2024-11-12 https://github.com/KennthShang/PhaBOX 2.1.11 phabox 2.1.12 To update Metagenomics Sequence assembly, Taxonomic classification, Visualisation Sequence assembly, Taxonomic classification, Visualisation Metagenomics, Microbial ecology, Sequence assembly, Taxonomy Metagenomics, Microbial ecology, Sequence assembly, Taxonomy ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox phabox PhaBOX Web server for identifying and characterizing phage contigs in metagenomic data. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
phi_toolkit_report phi_toolkit_report Phage host interaction toolkit report generator 2025-06-04 https://git.ufz.de/borimcor/phage-host-analysis 0.2.0 bioconductor-biostrings 2.74.0 To update Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pindel pindel Pindel detects genome-wide structural variation. 2021-09-29 http://artbio.fr 0.2.5b9 pindel 0.2.5b9 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plot_tools_astro_tool plot_tools_astro_tool Plot Tools 2024-11-22 0.0.1+galaxy0 pandas To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/plot-tools 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 https://workflowhub.eu/workflows/1369?version=1
pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS 2019-10-01 https://github.com/slhubler/PMD-FDR-for-Galaxy-P 1.4.0 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. 2016-11-04 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Variant Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. 2016-11-07 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Variant Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets 2017-09-22 http://artbio.fr 0.22.0 pysam 0.23.3 To update Sequence Analysis, Genomic Interval Operations, Graphics, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml 2015-01-24 0.1 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
proteomics_moff proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. 2017-12-11 https://github.com/compomics/moFF 2.0.3 moff 2.0.3 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 35 280 787 0 0 0 0 4 4 172 181 0 0 0 0 968 452 39 18
proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. 2021-09-16 https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 372 372 0 0 0 0 0 0 0 0 0 0 0 0 372 372 5 5
proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. 2021-09-16 https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 19 19 0 0 0 0 0 0 0 0 0 0 0 0 19 19 10 10
proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. 2021-10-13 https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 11 11 0 0 0 0 0 0 0 0 0 0 0 0 11 11 7 7
proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. 2021-06-30 https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html 0.0.8 proteomiqon-mzmltomzlite 0.0.8 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 723 723 0 0 0 0 0 0 0 0 0 0 0 0 723 723 10 10
proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. 2021-07-04 https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html 0.0.7 proteomiqon-peptidedb 0.0.7 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 96 96 0 0 0 0 0 0 0 0 0 0 0 0 96 96 12 12
proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. 2021-07-15 https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 686 686 0 0 0 0 0 0 0 0 0 0 0 0 686 686 5 5
proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. 2021-07-09 https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html 0.0.7 proteomiqon-proteininference 0.0.7 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 89 89 0 0 0 0 0 0 0 0 0 0 0 0 89 89 6 6
proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. 2021-07-09 https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html 0.0.8 proteomiqon-psmbasedquantification 0.0.9 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 604 604 0 0 0 0 0 0 0 0 0 0 0 0 604 604 4 4
proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. 2021-07-09 https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html 0.0.8 proteomiqon-psmstatistics 0.0.8 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 694 694 0 0 0 0 0 0 0 0 0 0 0 0 694 694 6 6
proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram 2021-05-17 2021.06.08 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 15 15 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1
protxml_to_xls protxml_to_xls 2015-01-24 0.1.0 trans_proteomic_pipeline To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
psm_eval psm_eval 2015-01-24 0.1.0 binaries_for_psm_eval To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
psm_to_sam PSMtoSAM PSM to SAM 2017-10-06 https://bioconductor.org/packages/release/bioc/html/proBAMr.html 1.3.2.1 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
psm_validation psmvalidator Validate PSM from Ion Fragmentation 2020-10-13 https://github.com/galaxyproteomics/psm_fragments.git 1.0.3 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 20 20 0 0 0 0 0 0 0 0 0 0 0 0 20 20 4 4
psy_maps psy_maps Visualization of regular geographical data on a map with psyplot 2019-03-15 https://github.com/Chilipp/psy-maps 1.3.1 python To update Visualization, Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 60 70 303 563 0 0 0 0 0 0 0 0 0 0 0 0 563 303 70 60 https://usegalaxy.eu/published/workflow?id=21363a774a7575f0, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://usegalaxy.eu/published/workflow?id=6df53b44018b2235, https://workflowhub.eu/workflows/1441?version=1 climate/climate-101
ptxqc maxquant_ptxqc Quality control reports for MaxQuant results 2025-04-16 https://github.com/cbielow/PTXQC 1.1.2 r-ptxqc To update Proteomics Validation Validation Proteomics Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ptxqc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ptxqc ptxqc PTXQC PTXQC is a quality control pipeline for proteomics results generated by MaxQuant. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. 2015-02-06 https://github.com/PyProphet/pyprophet 2.1.4 pyprophet 3.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 35 37 1794 2725 0 0 0 0 5 5 1052 1052 0 0 0 0 3777 2846 42 40 https://workflowhub.eu/workflows/1463?version=1 proteomics/DIA_Analysis_OSW
pyteomics mztab2tsv Tools using the pyteomics library 2021-01-15 https://pyteomics.readthedocs.io/en/latest/ 4.4.1 pyteomics 4.7.5 To update Proteomics, Metabolomics Protein identification Protein identification Proteomics, Proteomics experiment Proteomics, Proteomics experiment galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 93 93 0 0 0 0 0 0 0 0 0 0 0 0 93 93 5 5
quantp quantp Correlation between protein and transcript abundance 2018-09-13 1.1.2 r-data.table 1.11.6 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13 23 71 244 0 0 0 0 0 0 0 0 0 0 0 0 244 71 23 13
quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ 2020-01-21 https://sourceforge.net/projects/quantwiz/ 2.0 quantwiz-iq 2.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 4 26 57 0 0 0 0 0 0 0 0 0 0 0 0 57 26 4 2
query query Execute an SQL statement on a set of tables 2020-12-09 0.2 click To update Text Manipulation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type 2023-04-12 https://github.com/npinter/ROIsplitter 0.3.2 geojson To update Imaging galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 232 232 0 0 0 0 0 0 0 0 0 0 0 0 232 232 11 11
ramclustr ramclustr, ramclustr_define_experiment 2020-11-05 https://rdrr.io/cran/RAMClustR/ 1.3.1 r-ramclustr 1.3.1 Up-to-date Metabolomics Imputation, Standardisation and normalisation, Clustering, Correlation Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 36 36 103 103 15 15 37 37 3 3 707 707 42 42 304 304 1151 1151 96 96 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/1582?version=1 metabolomics/gc_ms_with_xcms
rawtools rawtools Raw Tools 2019-02-28 https://github.com/kevinkovalchik/RawTools rawtools 2.0.4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 44 72 204 0 0 0 0 15 16 522 550 0 0 0 0 754 594 60 50
rcx_boxplot rcx_boxplot recetox-boxplot is a tool for plotting boxplots from a tabular/csv/parquet data file. 2025-01-31 https://github.com/RECETOX/galaxytools 3.5.1 r-ggplot2 2.2.1 To update Visualization recetox https://github.com/RECETOX/galaxytools/tree/master/tools https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_boxplot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rcx_tk rcx-tk Tools to process metadata or alkane files. 2024-08-01 https://github.com/RECETOX/rcx-tk 0.1.0 rcx-tk 0.1.0 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
reactome_pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher 2018-06-08 https://github.com/LuisFranciscoHS/PathwayMatcher pathwaymatcher 1.9.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 70 95 127 280 0 0 0 0 0 0 0 0 0 0 0 0 280 127 95 70
recetox-aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. 2021-06-17 https://github.com/RECETOX/recetox-aplcms 0.13.4 r-recetox-aplcms 0.14.1 To update Metabolomics Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 7 7 1540 1540 0 0 0 0 1 1 410 410 3 3 928 928 2878 2878 11 11 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9
recetox-msfinder recetox_msfinder 2022-11-28 https://github.com/RECETOX/recetox-msfinder v3.5.2 To update Metabolomics Annotation Annotation Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 77 77 0 0 0 0 1 1 132 132 7 7 19 19 228 228 17 17 https://workflowhub.eu/workflows/888?version=2
recetox-xmsannotator recetox_xmsannotator_advanced 2021-07-13 https://github.com/RECETOX/recetox-xMSannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Up-to-date Metabolomics Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 9 9 0 0 0 0 3 3 184 184 0 0 0 0 193 193 5 5
regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text 2017-01-13 1.0.3 python To update Text Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 1008 1062 112043 114777 806 806 23975 23983 201 302 7586 9717 35 36 743 744 149221 144347 2206 2050 https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=1b72af1870c540d6, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, 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https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/363?version=2, https://workflowhub.eu/workflows/660?version=1 climate/pangeo, data-science/data-manipulation-olympics, digital-humanities/open-refine-tutorial, ecology/ENA_Biodiv_submission, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/biodiversity-data-exploration, ecology/ecoregiolifetraits, ecology/marine_omics_bgc, ecology/openrefine_gbif, ecology/phylogeny-data-prep, ecology/regionalGAM, genome-annotation/gene-centric, introduction/data-manipulation-olympics, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/metaquantome-data-creation, proteomics/neoantigen-fusion-database-generation, proteomics/neoantigen-non-reference-database-generation, proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-dbcreation, sequence-analysis/Manage_AB1_Sanger, single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, variant-analysis/trio-analysis
regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend 2019-06-18 https://github.com/RetoSchmucki/regionalGAM 1.5 r-mgcv To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 18 39 129 547 0 0 0 0 0 0 0 0 0 0 0 0 547 129 39 18 https://usegalaxy.eu/published/workflow?id=8e92a65d3307d87e, https://workflowhub.eu/workflows/1707?version=1 ecology/regionalGAM
rem_complex rem_complex Removes molecular coordination complexes. 2023-11-21 https://github.com/RECETOX/galaxytools 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 32 32 0 0 0 0 1 1 180 180 0 0 0 0 212 212 5 5 https://workflowhub.eu/workflows/888?version=2
rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results 2024-05-13 https://github.com/RECETOX/galaxytools/ 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 6 6 0 0 0 0 1 1 90 90 0 0 0 0 96 96 5 5 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9
repenrich edger-repenrich, repenrich Repeat element profiling 2017-05-22 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 42 1902 2173 0 0 0 0 2173 1902 42 39
repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner 2024-04-20 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
retip retip_apply, retip_descriptors, retip_filter_rt, retip_train 2020-09-07 https://github.com/PaoloBnn/Retip 0.5.4 To update Metabolomics Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers 2024-06-21 https://anaconda.org/conda-forge/r-bold 1.3.0 r-base To update Ecology ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 15 15 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8
retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format 2018-01-14 http://rest.ensembl.org/ 0.1.0 To update Data Source galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
revertr2orientationinbam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. 2019-04-17 0.0.2 samtools 1.22.1 To update SAM lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 60 60 37 37 637 637 0 0 0 0 0 0 0 0 697 697 49 49 https://usegalaxy.eu/published/workflow?id=6ebd09100fc98878, https://usegalaxy.eu/published/workflow?id=c98a14fcf5998159, https://usegalaxy.eu/published/workflow?id=d3494c6124f820b2, https://usegalaxy.eu/published/workflow?id=ef1d11b79a2e1727, https://usegalaxy.eu/published/workflow?id=fa53b172def3fe75, https://usegalaxy.org.au/published/workflow?id=5cd9b9338e75f254, https://usegalaxy.org/published/workflow?id=1f28e673ea725541, https://usegalaxy.org/published/workflow?id=53fdff74729a6780, https://usegalaxy.org/published/workflow?id=778a8867b0a6ea4f, https://usegalaxy.org/published/workflow?id=868acaf49d0743ec, https://usegalaxy.org/published/workflow?id=93e69c7e7a857ca3, https://usegalaxy.org/published/workflow?id=f3c8093c5b8a7233, https://workflowhub.eu/workflows/401?version=13
riassigner riassigner, riassigner_from_comment 2021-08-19 https://github.com/RECETOX/RIAssigner 0.4.1 riassigner 0.5.0 To update Metabolomics Standardisation and normalisation Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Metabolomics, Compound libraries and screening, Data submission, annotation and curation recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 75 75 5 5 16 16 1 1 178 178 27 27 161 161 430 430 62 62 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/1582?version=1 metabolomics/gc_ms_with_xcms
rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. 2021-02-25 https://github.com/MassBank/RMassBank 3.0.0 python To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 94 94 2 2 2 2 96 96 3 3
rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data 2017-12-18 https://github.com/deweylab/RSEM rsem 1.3.3 To update Transcriptomics, RNA artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 166 210 345 485 0 0 0 0 4 39 11 146 0 0 0 0 631 356 249 170
salmon_kallisto_mtx_to_10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 0.0.1+galaxy6 scipy To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 221 232 777 858 90 91 361 363 5 5 5 5 2 2 6 6 1232 1149 330 318 https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 single-cell/scrna-case_alevin
sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM 2020-05-19 http://artbio.fr 0.7.1+galaxy1 sambamba 1.0.1 To update SAM artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 1087 1087 0 0 0 0 1087 1087 25 25
saqc saqc, saqc_executor System for automated Quality Control 2025-01-13 https://git.ufz.de/rdm-software/saqc 2.6.0 saqc To update Statistics ufz https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/saqc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sashimi_plot sashimi_plot Generates a sashimi plot from bam files. 2019-08-21 http://artbio.fr 0.1.1 python To update RNA, Transcriptomics, Graphics, Visualization artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scaffold scaffold, scaffold_export 2015-01-24 0.1.0 scaffold To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scanpy_scripts anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. 2018-11-05 https://scanpy.readthedocs.io 1.9.3 scanpy-scripts 1.9.301 To update Transcriptomics, Sequence Analysis, RNA ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 27 27 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 14 13 0 456 501 45988 53754 223 223 12069 12159 48 48 3493 3493 0 0 0 0 69406 61550 772 727 https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b, https://usegalaxy.eu/published/workflow?id=5b8e4ae3447934d9, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83, https://usegalaxy.eu/published/workflow?id=73aa794916b91bb2, https://usegalaxy.eu/published/workflow?id=73b41b975da284d5, https://usegalaxy.eu/published/workflow?id=767f8c990316b66a, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=8f677efac7100097, https://usegalaxy.eu/published/workflow?id=9a0275211e74698a, https://usegalaxy.eu/published/workflow?id=9d15b328d8408715, https://usegalaxy.eu/published/workflow?id=ae79275d3568ad31, https://usegalaxy.eu/published/workflow?id=aeb0f5b74e51f5c2, https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514, https://usegalaxy.eu/published/workflow?id=decd6ad0b41289ef, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062, https://usegalaxy.eu/published/workflow?id=ffbbb905164d4c11, https://usegalaxy.org/published/workflow?id=802f5ff14a924e42, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1362?version=1, https://workflowhub.eu/workflows/1490?version=1, https://workflowhub.eu/workflows/1496?version=1, https://workflowhub.eu/workflows/1510?version=1, https://workflowhub.eu/workflows/1529?version=1, https://workflowhub.eu/workflows/1535?version=1, https://workflowhub.eu/workflows/1539?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1565?version=1, https://workflowhub.eu/workflows/1745?version=2, https://workflowhub.eu/workflows/467?version=4, https://workflowhub.eu/workflows/468?version=3, https://workflowhub.eu/workflows/512?version=2, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/646?version=2 imaging/multiplex-tissue-imaging-TMA, single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/scanpy_parameter_iterator, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata
sceasy sceasy_convert Convert scRNA data object between popular formats 2019-10-14 0.0.5 r-sceasy 0.0.7 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 301 310 1543 1615 103 104 521 522 5 5 349 349 1 1 2 2 2488 2415 420 410 https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 single-cell/EBI-retrieval, single-cell/scrna-case_alevin, single-cell/scrna-data-ingest
scripting tools singularity_scriptrunner suite_scripting 2023-07-29 https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ 0.3 To update Text Manipulation mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. 2024-03-29 https://cran.r-project.org/web/packages/sdmpredictors/index.html 0.2.15 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 4 4
sequence_format_converter sequence_format_converter various fasta to tabular conversions 2017-09-04 http://artbio.fr 2.2.0 python To update Convert Formats, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sgwb_astro_tool sgwb_astro_tool SGWB 2024-04-17 0.0.1+galaxy0 ipython To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 4 4 https://workflowhub.eu/workflows/815?version=2, https://workflowhub.eu/workflows/831?version=1
shift_longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees 2019-03-15 https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ 0.1.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 5 27 80 0 0 0 0 0 0 0 0 0 0 0 0 80 27 5 4
sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS 2016-10-11 0.2.4 sixgill 0.2.4 Up-to-date Proteomics, MetaProteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 37 41 167 320 0 0 0 0 0 0 0 0 0 0 0 0 320 167 41 37 https://usegalaxy.eu/published/workflow?id=799b924edd3c401b
small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files 2019-10-06 http://artbio.fr 1.3.0 pysam 0.23.3 To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
small_rna_maps small_rna_maps Generates small read maps from alignment BAM files 2017-07-23 http://artbio.fr 3.1.1 numpy To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. 2017-08-28 http://artbio.fr 3.4.2 pysam 0.23.3 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smithsonian_volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database 2019-04-15 https://volcano.si.edu/gvp_votw.cfm 0.1.0 python To update Retrieve Data climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
snv_matrix snvmatrix Generate matrix of SNV distances 2016-01-21 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza 2021-03-07 http://artbio.fr 3.0.0+galaxy1 sequenza-utils 3.0.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
source_extractor_astro_tool source_extractor_astro_tool Tool to extract luminous sources from astronomical sky images 2025-07-18 0.0.1+galaxy0 astropy To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/source-extractor 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7 7 0 0 0 0 0 0 0 0 0 0 0 0 7 7 2 2
spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. 2022-11-29 https://github.com/iomega/spec2vec 0.8.0 spec2vec 0.8.0 Up-to-date Metabolomics Spectrum calculation, Spectral library search, Database search, Natural product identification Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Proteomics experiment, Metabolomics, Natural language processing, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 176 176 0 0 0 0 177 177 2 2
spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files 2015-04-13 0.1.0 msproteomicstools 0.11.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files 2015-02-06 0.1.0 msproteomicstools 0.11.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spocc_occ spocc_occ Get species occurences data 2019-05-23 https://cran.r-project.org/web/packages/spocc/index.html 1.2.2 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 123 146 706 976 0 0 0 0 0 0 0 0 12 12 28 28 1004 734 158 135 https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/1670?version=1, https://workflowhub.eu/workflows/1687?version=1, https://workflowhub.eu/workflows/404?version=1 climate/earth_system, ecology/gbif_cleaning, ecology/species-distribution-modeling
sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads 2017-09-02 http://artbio.fr 2.3.1 bowtie 1.3.1 To update RNA, Next Gen Mappers Microbiology, Biology Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie sr_bowtie sr_bowtie Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 98 98 0 0 0 0 0 0 0 0 98 98 2 2
sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. 2017-09-11 http://artbio.fr 2.8 bowtie 1.3.1 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 2022-11-16 0.0.1 r-base To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 8 8 274 274 5 5 48 48 0 0 0 0 3 3 22 22 344 344 16 16 https://usegalaxy.eu/published/workflow?id=1d2cd0af01a30a46, https://usegalaxy.eu/published/workflow?id=da88448ab15d167d, https://workflowhub.eu/workflows/1669?version=2, https://workflowhub.eu/workflows/657?version=1 ecology/remote-sensing
stoceps stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. 2019-09-26 0.0.2 To update Ecology ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 24 26 180 354 0 0 0 0 0 0 0 0 0 0 0 0 354 180 26 24 https://usegalaxy.eu/published/workflow?id=01274dfdbdfcaa88
suite_cell_types_analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis 2020-04-07 1.1.1 cell-types-analysis 0.1.11 To update Transcriptomics, RNA, Statistics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 4 4 https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d
suite_celltypist celltypist_predict celltypist - Automated cell type annotation 2025-02-14 https://celltypist.readthedocs.io/en/latest/ 1.6.3+galaxy1 celltypist 1.7.1 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/celltypist 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities 2023-09-24 https://decoupler-py.readthedocs.io/en/latest/ 1.4.0+galaxy3 decoupler 1.5.0 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 157 157 5 5 37 37 1 1 3 3 2 2 6 6 203 203 20 20 https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1556?version=1 single-cell/pseudobulk-analysis
suite_dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 2019-01-22 1.0.4 dropletutils-scripts 0.0.5 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 290 306 2109 2283 126 127 717 720 3 3 5 5 1 1 4 4 3012 2835 437 420 https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=95fe49cafa1dff7e, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=dc9bfa4f633c49b4, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f474eb2f45f1d684, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1523?version=1, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 single-cell/scrna-case_alevin, single-cell/scrna-data-ingest
suite_ebi_expression_atlas retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home 2019-07-02 v0.0.2+galaxy2 wget To update Transcriptomics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264 301 1075 1259 155 155 448 448 13 13 145 145 4 4 13 13 1865 1681 473 436 https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=dd73bdcbac8649a3, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1535?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1552?version=1, https://workflowhub.eu/workflows/1570?version=1 single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-case_basic-pipeline
suite_garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 2020-04-03 0.2.8 garnett-cli 0.0.5 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 25 27 0 0 0 0 0 0 0 0 0 0 0 0 27 25 4 3 https://usegalaxy.eu/published/workflow?id=8762437178c9a3cf, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d
suite_human_cell_atlas_tools hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects 2019-07-02 v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 To update Transcriptomics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 87 114 431 566 1 2 2 3 0 0 0 0 0 0 0 0 569 433 116 88 https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83 single-cell/EBI-retrieval
suite_monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. 2019-09-09 0.1.4 monocle3-cli 0.0.9 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 76 81 3733 3956 60 61 1939 1971 0 0 0 0 0 0 0 0 5927 5672 142 136 https://usegalaxy.eu/published/workflow?id=35c092316cdc27d1, https://usegalaxy.eu/published/workflow?id=8762437178c9a3cf, https://usegalaxy.eu/published/workflow?id=a3a7c1853ae7047b, https://usegalaxy.eu/published/workflow?id=a7fcfab658a2cc33, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d, https://usegalaxy.eu/published/workflow?id=f689faf267fbe504, https://workflowhub.eu/workflows/1516?version=1, https://workflowhub.eu/workflows/1524?version=1, https://workflowhub.eu/workflows/1531?version=1 single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest
suite_ogs ogs_addlayer, ogs_extractboundary, ogs_extractsurface, ogs_generatestructuredmesh, ogs_identifysubdomains, ogs_simulation A suite of tools for OpenGeoSys (ogs) 2025-03-06 https://gitlab.opengeosys.org/ogs/ogs 6.5.3 To update Geo Science ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_ogs_tools msh2vtu, shp2msh A suite of tools for OpenGeoSys (ogs) 2025-03-03 https://gitlab.opengeosys.org/ogs/tools/ogstools 0.4.0 ogstools To update Geo Science ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ 2024-08-20 0.12.1 To update Transcriptomics, RNA, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. 2018-11-05 1.8.0 sc3-scripts 0.0.6 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 6 9 13 0 0 0 0 0 0 0 0 0 0 0 0 13 9 6 4
suite_scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. 2018-10-11 1.10.0 scater-scripts 0.0.5 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 67 80 254 398 5 5 18 18 7 8 387 429 0 0 0 0 845 659 93 79 https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8, https://usegalaxy.org.au/published/workflow?id=3c9140288202aa76, https://workflowhub.eu/workflows/1511?version=1 single-cell/scrna-scater-qc
suite_scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. 2019-08-30 1.6.4 scmap-cli 0.1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 105 114 0 0 0 0 0 0 0 0 0 0 0 0 114 105 11 11 https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=95fe49cafa1dff7e, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=dc9bfa4f633c49b4
suite_scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 2020-04-07 1.0.2 scpred-cli 0.1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 25 25 0 0 0 0 0 0 0 0 0 0 0 0 25 25 2 2 https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=f474eb2f45f1d684
suite_seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 2018-07-09 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 4.0.0 seurat-scripts 4.4.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 124 154 5535 5985 155 155 3504 3504 9 9 563 563 4 4 106 106 10158 9708 322 292 https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=10c5d0560b977a6f, https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958, https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf, https://usegalaxy.org/published/workflow?id=59554bfcad77e307, https://workflowhub.eu/workflows/1527?version=1, https://workflowhub.eu/workflows/1535?version=1, https://workflowhub.eu/workflows/1555?version=1, https://workflowhub.eu/workflows/1560?version=1, https://workflowhub.eu/workflows/1570?version=1 single-cell/EBI-retrieval, single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-data-ingest, single-cell/scrna-seurat-pbmc3k
suite_snvphyl_1_2_3 SNVPhyl suite defining all dependencies for SNVPhyl 2015-08-05 To update Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tables table_pandas_arithmetics, table_pandas_rename_column, table_pandas_rename_columns_regex, table_pandas_transform, table_scipy_interpolate Tools to manipulate and analyze data tables. 2024-11-14 https://github.com/RECETOX/galaxytools scipy To update Metabolomics, Statistics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/tables https://github.com/RECETOX/galaxytools/tree/master/tools/tables 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 78 718 718 0 0 0 0 0 0 0 0 0 0 0 0 718 718 78 78
tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files 2021-05-05 http://artbio.fr 0.6.1 pigz To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
terrabyte_ogc_api_processes terrabyte_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/). 2024-11-11 https://github.com/AquaINFRA/galaxy 0.1.0 r-base To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/terrabyte_ogc_api_process https://github.com/galaxyecology/tools-ecology/tree/master/tools/terrabyte_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2
thermo_raw_file_converter thermo_raw_file_converter Thermo RAW file converter 2018-09-14 https://github.com/compomics/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 To update Proteomics Conversion, Filtering, Peak detection Conversion, Filtering, Peak detection Proteomics, Proteomics experiment, Metabolomics Proteomics, Proteomics experiment, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser ThermoRawFileParser ThermoRawFileParser Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 99 146 2568 3222 0 0 0 0 21 21 1294 1326 0 0 0 0 4548 3862 167 120 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9
topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. 2021-12-23 https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7 7 74 74 5 5 25 25 0 0 0 0 0 0 0 0 99 99 12 12 https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1
translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames 2018-01-14 http://rest.ensembl.org/ 0.1.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 185 200 697 914 123 123 505 505 27 27 1081 1081 0 0 0 0 2500 2283 350 335 https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation
translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column 2016-01-13 0.2.0 biopython 1.70 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 23 37 72 0 0 0 0 0 0 0 0 0 0 0 0 72 37 23 14
ucsc_cell_browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets 2018-09-11 https://cells.ucsc.edu/ 1.0.0+galaxy1 ucsc-cell-browser 1.2.15 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 148 189 731 1002 0 0 0 0 0 0 0 0 0 0 0 0 1002 731 189 148 https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062
unipept unipept Unipept retrieves metaproteomics information 2015-04-03 https://github.com/galaxyproteomics/tools-galaxyp 6.2.4+galaxy0 python To update Proteomics Prediction and recognition, Visualisation Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows Proteomics, Proteogenomics, Biodiversity, Workflows galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 282 314 4723 6047 102 102 384 384 33 33 1383 1383 1 1 1 1 7815 6491 450 418 https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=50d85103f2275d38, https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6da171871d4f3fd5, https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e, https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1443?version=1, https://workflowhub.eu/workflows/1450?version=1, https://workflowhub.eu/workflows/1482?version=1 microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/metaproteomics, proteomics/metaquantome-data-creation
uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format 2016-03-08 https://www.uniprot.org/help/programmatic_access 2.5.0 requests To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 313 1805 2133 73 73 143 143 41 41 1139 1139 0 0 0 0 3415 3087 427 353 https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-3-verification
upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server 2022-01-18 0.0.5 omero-py 5.11.1 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. 2017-09-14 0.1.5 validate-fasta-database 1.0 To update Fasta Manipulation, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 414 414 39 39 148 148 9 9 164 164 0 0 0 0 726 726 116 116 https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1793?version=1 proteomics/neoantigen-fragpipe-discovery
varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. 2022-11-28 http://artbio.fr 0.1 python To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls 2016-01-20 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
verify_map verify_map Checks the mapping quality of all BAM(s) 2015-05-15 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
vibrant vibrant Virus Identification By iteRative ANnoTation 2024-09-11 https://github.com/AnantharamanLab/VIBRANT 1.2.1 vibrant 1.2.1 Up-to-date Metagenomics Sequence trimming, Scaffolding, Genome annotation Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 1586 1586 0 0 0 0 0 0 0 0 0 0 0 0 1586 1586 65 65 https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95
vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. 2019-03-13 https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro 0.1.1 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 258 284 14141 17115 0 0 0 0 0 0 0 0 0 0 0 0 17115 14141 284 258 https://usegalaxy.eu/published/workflow?id=596b073ab7249aa2, https://usegalaxy.eu/published/workflow?id=c0888e0a0fb53ed3
virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. 2024-06-20 https://github.com/jiarong/VirSorter2/ 2.2.4 virsorter 2.2.4 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter virsorter virsorter Identify DNA and RNA virus sequences. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 144 144 2379 2379 0 0 0 0 0 0 0 0 0 0 0 0 2379 2379 144 144 https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95
vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations 2019-10-24 https://www.ks.uiuc.edu/Research/vmd/ To update Computational chemistry chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. 2021-02-10 https://github.com/RECETOX/WaveICA 0.2.0 r-recetox-waveica 0.2.1 To update Metabolomics Standardisation and normalisation Standardisation and normalisation Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 58 58 6 6 8 8 2 2 538 538 4 4 13 13 617 617 21 21 https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 metabolomics/gc_ms_with_xcms
wisecondorx wisecondorx_npz_converter, wisecondorx_predict, wisecondorx_reference_builder WisecondorX 2024-12-15 https://github.com/CenterForMedicalGeneticsGhent/WisecondorX/tree/master 1.2.9 wisecondorx 1.2.9 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/wisecondorx https://github.com/ARTbio/tools-artbio/tree/main/tools/wisecondorx 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
wtv wtv A cli/python library for ion selection in mass spectrometry. 2025-06-02 https://github.com/RECETOX/wtv 0.1.0 wtv 0.1.0 Up-to-date Metabolomics Feature selection Feature selection Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/wtv https://github.com/RECETOX/galaxytools/tree/master/tools/wtv wtv wtv A CLI/python library that selects characteristic qualitative ions based on https://github.com/yuanhonglun/WTV_2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. 2020-05-06 http://xarray.pydata.org 2022.3.0 xarray To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 132 133 6057 6116 12 12 113 113 2 2 436 436 4 4 18 18 6683 6624 151 150 https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=6df53b44018b2235, https://usegalaxy.eu/published/workflow?id=7b50e72deb46c6e8, https://usegalaxy.eu/published/workflow?id=a0eff33b83ac1d1e, https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3, https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612, https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7, https://workflowhub.eu/workflows/1427?version=1, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1436?version=1, https://workflowhub.eu/workflows/1652?version=1 climate/argo_pangeo, climate/fates, climate/pangeo, ecology/x-array-map-plot
xarray_import_data xarray_import_data A data import tool for opening OPeNDAP datasets and storing as netCDF files. 2025-08-14 http://xarray.pydata.org 0.1.0 xarray To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 8 8 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 https://usegalaxy.eu/published/workflow?id=a0eff33b83ac1d1e
xlsx2tsv xlsx2tsv Convert an xlsx file to a tabular 2024-12-16 https://github.com/Helmholtz-UFZ/galaxy-tools 0.1.0+galaxy0 pandas To update Text Manipulation ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/xls2tsv https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/xls2tsv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60 60 490 490 0 0 0 0 0 0 0 0 0 0 0 0 490 490 60 60
xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another 2021-10-18 1.6.1 xmlstarlet To update Convert Formats ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 102 102 0 0 0 0 0 0 0 0 3 3 3 3 105 105 21 21 https://usegalaxy.eu/published/workflow?id=8a81615501be20fd, https://usegalaxy.eu/published/workflow?id=f98560da584d5abf
xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing 2021-05-26 https://github.com/GoekeLab/xpore 2.1+galaxy0 xpore 2.1 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
xtb_molecular_optimization xtb_molecular_optimization Performs semiempirical molecular optimization. 2023-08-24 https://github.com/grimme-lab/xtb 6.6.1 xtb To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2773 2773 0 0 0 0 2 2 177 177 0 0 0 0 2950 2950 12 12 https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e, https://usegalaxy.eu/published/workflow?id=5465916d9b51f411, https://workflowhub.eu/workflows/1597?version=1, https://workflowhub.eu/workflows/897?version=3 metabolomics/qcxms-predictions
yac_clipper yac Clips 3' adapters for small RNA sequencing reads. 2015-06-17 http://artbio.fr 2.5.1 python To update RNA, Fastq Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems 2024-06-29 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 54 54 0 0 0 0 0 0 0 0 0 0 0 0 54 54 3 3
zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. 2024-05-03 https://github.com/AquaINFRA/galaxy 0.1.0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 28 28 0 0 0 0 0 0 0 0 0 0 0 0 28 28 5 5 https://usegalaxy.eu/published/workflow?id=e95bfab07fdec632