Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on BioBix	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on MISSISSIPPI	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)
2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	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	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	6541
2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	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	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	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	1	1	0	19	13760
2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	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	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	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	1	1	0	18	6834
2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	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	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	656
2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	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	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	6156
3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	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	3	3	0	47	2889
GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	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	1	1	0	0	45
TreeBest	treebest_best	TreeBeST best	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.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	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	1	1	0	23	984
abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	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
anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	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	0.4.0	medpy	0.4.0			0	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	1	1	0	0	40
apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	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	1	1	0	1	3
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								To update	https://github.com/galaxy-genome-annotation/python-apollo	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		apollo	4.2.13			0	0	9	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	9	9	0	301	1896
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/								To update	https://github.com/askomics/	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		askocli	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	0	0	0
askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			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
background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	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
bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	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.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			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
baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	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	1.1.0					0	0	0	2	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
batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			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
bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	1523
binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	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	1	1	0	34	1273
binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	0	29
bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	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	9
biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			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	0	0	0	0	0	0	0
biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	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_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	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	1	1	0	27	296
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 .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	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	1	0	0	17	109
braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567
bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0
camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	30	623
cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			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
collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	1	0	0	0	1	1	0	1583	33934
color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	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	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	1	16
colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	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	3.2.1	networkx				0	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
combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	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_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	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	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	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	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	3	78
concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	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
coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	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	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	8	16546
correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	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
count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	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	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25	272
cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to in-silico determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	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	1	1	0	16	8518
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								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0
curl_post	curl_post	Send file via cURL POST								To update	https://github.com/bmcv	Data Export, Web Services	curl_post	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	0.0.2	curl				0	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	1	1	0	27	440
curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	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	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	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	1	0	0	1	12
detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	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	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	2	46
ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	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	1	0	0	53	9907
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	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	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899
export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	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								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			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	0	0	0
fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	10
fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			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	0	0	0
feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			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	0	0	0
feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	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
filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			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
gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	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
gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	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	0	0	0	0	0	0	0
gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	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								Up-to-date	https://genenotebook.github.io	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	0.4.16	genoboo	0.4.16			0	0	1	1	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
genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	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	1	1	0	0	68
get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			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
gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	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
gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	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	1	1	0	4	397
hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	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	1	1	0	13	238
hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	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	1	1	0	7	290
helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93
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.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			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
image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	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	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	41	621
image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	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	1.26.4	numpy				0	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
image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	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	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	0	0	2	12
imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	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	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	7	21825
influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	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	1.0.2	influx-si-data-manager	1.0.3			0	0	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
influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	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
ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	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								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2
jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	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		python				0	0	0	0	0	0	0	0	0	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.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			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
kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			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
kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			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
kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	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	1.0.0	python				0	0	0	0	0	0	0	0	0	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	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	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	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	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
labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	0	36
landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	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	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	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	1	1	0	9	857
logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			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	0	0	0
lotus2	lotus2	LotuS2 OTU processing pipeline	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.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	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	1	0	0	114	936
mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	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	0.7-2	mahotas				0	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	1	1	0	0	37
mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	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								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			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
mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	0	25
metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	153
metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	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	1	0	0	6	12
miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	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	41	6076
miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	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								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	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
mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	322	89021
morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	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	1.12.0	scipy				0	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
mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			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
ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	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
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								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	11	0	0	10	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	40	709
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								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	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
mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	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_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					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
ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	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	0.5.0					1	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
nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	47
nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	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
nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	4	140
normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	133
openlabcds2csv	openlabcds2csv	Creates a summary of several "Internal Standard Report" OpenLabCDS results.								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	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			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	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
overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	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	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60
pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	0	259	7276
patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	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								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	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
permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	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	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	0	42
physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	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
physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	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
plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	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.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	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
plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				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
plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	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
plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	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
plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	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
pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			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	0	0	0	0	0	0	0
points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	2	41
points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	0	31
points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	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	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	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	1	0	0	2	29
projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	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	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	1	85
projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	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	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	9	21343
promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	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.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			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	0	0	0
quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	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
rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	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.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	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
repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	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	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	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
repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	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	2.3.8					0	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	16
replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	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	1	1	0	20	537
rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	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.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	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	7
rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	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	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	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	1	1	0	9	512
segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			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
segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	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	1	0	0	2	3
seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			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
sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	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	1	1	0	133	2489
skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	1	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
slice_image	ip_slice_image	Slice image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	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	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	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	1	1	0	0	102
smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			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
smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			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	0	0	0
smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	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	1	1	0	9	493
spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	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
spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	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	0	0	0	0
split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	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	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	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	1	1	0	0	42
spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	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
spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	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	0.0.3-2	imageio		Image analysis	Imaging, Bioinformatics	0	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	1	0	0	3	16
srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	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	1	0	0	22	205
staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	889	12673
stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			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
suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13
suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5
suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67
suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202
suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73
suite_qiime2__demux	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									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114
suite_qiime2__diversity	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									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168
suite_qiime2__diversity_lib	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									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4
suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6
suite_qiime2__feature_classifier	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									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263
suite_qiime2__feature_table	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__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									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213
suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20
suite_qiime2__longitudinal	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									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14
suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232
suite_qiime2__phylogeny	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									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37
suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, 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									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0
suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13
suite_qiime2__rescript	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_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					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
suite_qiime2__sample_classifier	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									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1
suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172
suite_qiime2__vsearch	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									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16
suite_qiime2_core										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
suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		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	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087
superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	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.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	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	1	0	0	2	16
t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	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	1	1	0	70	8690
tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	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	1.1.0	perl-bioperl	1.7.8			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
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								To update	https://github.com/galaxy-genome-annotation/python-tripal	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		python-tripal	3.2.1			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	0	0	0	0	0	0	0
unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	508	5370
visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	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	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	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	1	1	0	0	25
voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	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	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	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
w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	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	1	1	0	3	2834
w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	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
w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	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	1	1	0	5	368
w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	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	1	1	0	2	171
wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			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	0	0	0	0	0	0	0
wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	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	0.2-2	scikit-image				0	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	1	1	0	0	38
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		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.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	12	9	11	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	9	0	356	29809
10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	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	1	0	0	46	228
AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	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	1	1	0	6	116
AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	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	1	0	10	3060
CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	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	1	1	0	14	45191
CollectResults	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%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	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	1	1	0	14	1961
CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	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	1	1	0	0	108
GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	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	1	1	0	4	133
LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	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	1	1	0	13	45325
NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	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	2	2	0	28	62388
Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	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	1	1	0	3	68
PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	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	1	1	0	15	1932
Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	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	1	1	0	18	1758
Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	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	1	1	0	16	2925
add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	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	1	0	0	193	14480
add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	0	0	1	1	0	1	1	1	1	591	367167
agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481
align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	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	0.0.10	biopython	1.70			0	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	1	1	0	11	329
annotation_profiler	Annotation_Profiler_0	Profile Annotations for a set of genomic intervals								To update		Genomic Interval Operations	annotation_profiler	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler	https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler	1.0.0	bx-python	0.13.0			1	0	1	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	1	1	0	0	2
antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	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	1	1	0	2	52
antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	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.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	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	1	1	0	279	14596
aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	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	1	1	0	4	65
atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	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	1	1	0	26	257
augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	516	8864
bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	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	1	1	0	15	169
barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	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								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	2	308
best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	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	1.0.0	numpy				1	0	1	1	1	0	1	1	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
bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	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	2
bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	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
biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	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	13
bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	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	1	0	0	112	531
bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	4	4	0	332	12876
blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	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	1.0.0					0	0	0	0	0	0	0	0	0	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								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	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.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	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	1	0	0	21	685
blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	34	3009
blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	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	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	15	1478
bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	506	22988
canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	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	1.0.0	R				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	74
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).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	533	13021
categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	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	1.0.0					0	1	1	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	1	1	0	1	40
ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	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	1	1	0	15	173
cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	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	0.0.1	cd-hit-auxtools	4.8.1			1	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
cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	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
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	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	19	0	178	4614
cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	8	43
change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	1	1	0	1	1	1	1	931	10965
chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	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
chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	418	15690
chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	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)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	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	1	1	0	8	251
clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	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	0.0.7	samtools	1.21			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	0	0	0	0	0	0
clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	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.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	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
cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	1	801
cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	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	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	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	1	0	0	1	102
cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	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	2	2	0	1	108
cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	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	1	1	0	8	342
column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	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	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	179	3781
combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	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	1	0	0	9	147
compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	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	1	1	0	0	220
compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	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	332
complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	1	233
compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	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	1.0.0					0	1	1	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	1	1	0	2	94
compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	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	1.0.0					0	1	1	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	1	1	0	0	65
compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	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	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35
concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	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	1.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	1	1	0	309	564900
condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	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
convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	1	1	0	1	1	1	1	475	23829
convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			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
correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	47	837
count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	271
count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			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
coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	17	1502
coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			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
cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	134
crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	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	1	1	0	74	3389
ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	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	1	1	0	13	203
cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	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	1	1	0	31	1782
cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	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	1	1	0	13	1204
cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	1	1	0	1	1	1	1	5064	1957541
delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	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	1.0.0					0	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	1	1	0	2	39
dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	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	1	0	0	11	72
dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	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	1	1	0	7	65
diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	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	1	1	0	30	235
diffbind		Diffbind provides functions for processing ChIP-Seq data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	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
divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	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	1.0.0					1	0	1	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	1	1	0	0	32
dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	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	1	0	0	1	1576
dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			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
dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	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	1	0	0	1	83
draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	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	1.0.0	R				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	12	173
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								To update		Statistics	dwt_cor_ava_perclass	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	1.0.1	r-waveslim	1.7.5			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
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								To update		Statistics	dwt_cor_avb_all	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	1.0.1	r-waveslim	1.7.5			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
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								To update		Statistics	dwt_ivc_all	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	1.0.1	r-waveslim	1.7.5			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
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								To update		Statistics	dwt_var_perclass	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	1.0.1	r-waveslim	1.7.5			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
dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	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	1.0.2	r-bitops				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36
ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	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
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.	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.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	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	1	0	0	58	484
effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence 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
epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	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	1	1	0	5	245
exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	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
express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	12	325
fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	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	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	380	7758
fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	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	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	88	35793
fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	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	0.0.7	galaxy_sequence_utils	1.1.5			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
fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	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	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	350	48649
fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	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	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	622	105935
fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	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	0.0.7	galaxy_sequence_utils	1.1.5			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
fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	679	5765
fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	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	0.0.5	galaxy_sequence_utils	1.1.5			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
fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	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	0.1.5	galaxy_sequence_utils	1.1.5			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
fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	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	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	459	5676
fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	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	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	6	22385
file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	176	8496
filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	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	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	20
find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	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	1.0.0	taxonomy	0.10.0			0	0	1	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	1	1	0	5	69
find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	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	1	1	0	31	763
flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	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	4.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	20	671
flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	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
flye	flye	Assembly of long and error-prone reads.	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. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	1	1	0	1499	20904
footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	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	1	1	0	0	57
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								To update		Fasta Manipulation	format_cd_hit_output	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	1.0.0+galaxy1					0	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	1	1	0	20	166
format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	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).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	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	1	1	0	166	5588
generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	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	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	119
get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	555	324598
get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	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	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	15	186
getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	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	bx-python	0.13.0			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
getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	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	numpy				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
gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	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.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	Data handling	Computational biology	1	1	1	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	1	0	0	418	8159
gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	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).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	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	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	27	660
glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	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
gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	11
gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	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	1	1	0	1	71
graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	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.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	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	6
graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	43	2605
graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads \| GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	136	6651
graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	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	1	1	0	6	474
hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis	hgv_fundo	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	1.0.0					1	0	1	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	1	1	0	0	0
hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	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	1.0.0	R				1	0	1	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	1	1	0	0	0
hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	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
hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	76	921
hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				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	228
histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	242	4350
homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	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
htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	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	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	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	1	0	0	15	77
illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	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_enhance_contrast, 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.	imagej	imagej	imagej2	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.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20170530			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537
improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	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	0	0	0	0	0	0	0	0
indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	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	1	1	0	0	22
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.	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.	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	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	6	6	0	67	100294
inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	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
instagraal	instagraal	Large genome reassembly based on Hi-C data	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)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	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	1	0	0	14	139
intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	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	1	1	0	23	7569
intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	1003	348449
iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	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
itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	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.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	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	1	0	0	38	868
jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	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
join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	284	329556
join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	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	1.0.1	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	117	2448
jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	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	30
kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	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	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	69
kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	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	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	156
kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	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
kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	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	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	481	14683
labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	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
lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	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	1.1.1	lastz	1.04.22			0	1	1	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	1	1	0	1	9
lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	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	1.0.1	taxonomy	0.10.0			0	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	1	1	0	2	137
lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	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	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	148
lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	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.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	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	1	1	0	9	152
linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				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
locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	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	1	1	0	11	339
logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	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	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	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	bx-python	0.13.0			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
mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	2	0	0	0	2	2	0	817	143045
mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	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	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	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
mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	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	1	1	0	3	85
megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	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	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	36	338
merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	193	563676
merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	0	0	1	1	0	1	1	1	1	542	28593
methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	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	5461
methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	200	16573
methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	1	0	0	0	1	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
metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	1	1	0	103	3966
mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	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	sputnik				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
microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			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
minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	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	1	1	0	53	895
mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	11
minipolish	minipolish	Polishing miniasm assemblies	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.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	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	1	0	0	21	185
mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	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	1	0	0	56	613
molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	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.	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.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	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
mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	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	1	1	0	5	76
multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	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	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	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								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	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	1	1	0	83	652
music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	240	1872
mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	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	1.0.0					1	0	1	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	1	1	0	0	47
nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	4	4	0	78	8366
nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	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	1	1	0	0	40
netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	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	1	0	0	5	11
nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	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.	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	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	1	0	0	84	268
nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			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	0	0	0
nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	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	1	1	0	2	861
numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	486
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.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	134	0	916	105743
pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	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	1	1	0	7	269
paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	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	1	1	0	7	299
partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	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	R				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
peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	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	1	1	0	78	3109
pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165
pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	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								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	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	1	0	0	14	82
pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	15	632
pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	169	3158
pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	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	1	1	0	21	275
piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	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	1	1	0	39	1809
platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	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
plot_from_lda	plot_for_lda_output1	Draw ROC plot on "Perform LDA" output								To update		Graphics, Statistics	plot_from_lda	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	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	73
plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	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	0.4	galaxy-ml	0.10.0			1	1	1	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	1	1	0	71	1323
plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	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	0.2	python				1	1	1	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	1	1	0	37	652
plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	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	0.1	python				1	1	1	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	1	1	0	79	843
poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	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	1.0.0	taxonomy	0.10.0			0	1	1	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	1	1	0	6	116
predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					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	0	0	0	0	0	0	0
principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	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	1.0.2	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	88	9989
protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	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	1	1	0	7	154
protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	451	6428
protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	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	1	1	0	30	604
quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	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.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	309	21353
rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	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	36
rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	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	1	1	0	38	1226
rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				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
reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	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
remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	0	0	1	1	0	1	1	1	1	1409	137310
remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	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	1	1	0	2	42
repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	248	3750
replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	1	0	189	576111
rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	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	3	3	0	44	628
rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	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	0	0	0	0	0	0	0
rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	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	0	0	0	0	0	0	0
rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	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	3.3.0	@EXECUTABLE@				0	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	1	1	0	11	129
rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	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	1	1	0	3	164
rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	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	1	1	0	5	1358
rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	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	0.1.1	sam	3.5			0	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	1	1	0	6	1074
rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	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
rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	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	1	1	0	4	33
rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	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	1	1	0	5	86
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.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279
sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	55	4024
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.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	2	0	0	0	3	3	0	969	61937
sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	1189
sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	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	1.0.1	python				1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	278
sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	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
sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	149	3765
samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			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	0	0	0	0	0	0
samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	1	1	1	296	4948
samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	1450	48426
scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	61	1677
sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	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	2	2276
segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	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	1	1	0	30	1276
selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	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	1	1	0	27	457
seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874
seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	306	25302
seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	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	0.0.8	biopython	1.70			0	0	1	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	1	1	0	82	3784
seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			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
seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	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	0.0.18	galaxy_sequence_utils	1.1.5			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
seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			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	1	0	0	0
seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	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	0.0.15	biopython	1.70			0	1	0	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
short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	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	1.0.0	rpy				0	0	0	0	0	0	0	0	0	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								To update		Sequence Analysis, Graphics	short_reads_figure_score	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	1.0.2	fontconfig				0	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	1	1	0	13	163
short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	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	1.0.0					1	0	1	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	1	1	0	21	220
show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	0	1	1	0	0	1	1	0	1	1	1	1	704	32112
show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	0	1	1	0	0	1	1	0	1	1	1	1	128	2513
sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	0	5	374
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								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	27	0	958	113932
snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	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	1.0.1	R				1	1	1	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	1	1	0	7	37
sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	376	18183
split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	159	5507
split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	1	0	412	15358
split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					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
splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	96	1295
sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	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	1	1	0	5	223
statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	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	1	0	0	21	304
stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47
substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			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
subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	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	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	182	564229
subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	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	0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	55	1019
t2ps	Draw_phylogram	Draw phylogeny	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	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	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	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	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	1	1	0	31	457
t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	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	1.0.0	taxonomy	0.10.0			0	0	1	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	1	1	0	26	947
t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	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	1.0.1	R				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	210
table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	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
tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_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	1.0.0	perl				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	14	2207
tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	1	1	0	601	319334
tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	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
targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	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	1	1	0	37	713
text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	20	20	20	20	20	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	20	0	0	0	19	19	0	15048	3864895
tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	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.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	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	1	0	0	36	460
tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	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).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	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	1	1	0	15	445
tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			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	1	0	0	0	0	0	0	1
tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	1	0	312	24167
tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	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	blast+				0	1	1	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	1	1	0	15	216
trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	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.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	2334	238699
trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	0	0	1	1	0	1	1	1	1	188	6058
trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	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	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	2	0	0	0	2	2	0	236	2935
ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	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	python				1	0	1	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	1	1	0	45	394
uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	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	1	1	0	132	2406
varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	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	2.4.2	varscan	2.4.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	246	5191
vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	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	1	1	0	15	206
vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					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
vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	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	1	1	0	63	388
vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	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	19
vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	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	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	171
vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	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	0.1	tabix	1.11			0	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	1	1	0	34	531
vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	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	0.1.11	samtools	1.21			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
vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	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	0.1.1	tabix	1.11			0	1	1	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	1	1	0	35	498
vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	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	0.1.11	tabix	1.11			0	1	1	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	1	1	0	68	953
vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	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	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	411
vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	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	0.1	tabix	1.11			0	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	1	1	0	17	137
venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	248	5067
vienna_rna	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								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	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	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864
vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			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	0	0	0	0	0	0	0
weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	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
whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	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
windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			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	11
woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	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
wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	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.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	116	1660
xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	344	5892
TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	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	1	0	0	8	42
abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	3	3	0	1764	496717
abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	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.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	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
abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	391	4278
adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	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.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	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	1	0	0	37	217
add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	91	83150
aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	47	168
aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	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.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	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	1	0	0	13	129
allegro	allegro	Linkage and haplotype analysis from deCODE	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.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	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
amplican	amplican	AmpliCan is an analysis tool for genome editing.	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.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	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	1	0	0	12	53
ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, 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	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267
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.	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	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	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	591
ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	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.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	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	1	0	0	4	7
anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	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	5	5	0	625	35620
annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	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.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	1175	25975
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	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.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	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
arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	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	3	0	0	38	3528
art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	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	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	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	0
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	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	1	0	123	8175
assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	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
astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			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
augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	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.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	2	2	0	685	11245
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.	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	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	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	1	0	0	12	345
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."	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	151	2982
bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	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	1	1	0	4	128
bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	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	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	0	208	14021
bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	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	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1195	114863
bamtools_split	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.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		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	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	4	0	0	197	4328
bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	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	1	0	0	8	39
bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	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.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	2	0	0	0	2	2	0	2016	44390
barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			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	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.	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.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71
barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	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).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	160	3938
basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	35	266
bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	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	1	1	0	8	200
bayescan	BayeScan	Detecting natural selection from population-based genetic data	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.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	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	1	1	0	8	64
bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	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
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.	bbmap	bbmap, bbtools		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.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.08	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	4	0	0	420	6381
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	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.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	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								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	87	2895
beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	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	3	0	0	0	28
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.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	To update	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.3	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	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	0	0
beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	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	1	0	0	10	54
bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	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	1	0	0	10	28
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	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	37	37	37	37	37	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	37	0	0	0	37	37	0	5844	901750
bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	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	1	0	0	123	1194
berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			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
bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	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.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	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
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	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	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
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.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	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	1	0	0	21	81
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!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	2	0	0	363	15228
bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	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	1	0	0	71	978
biom_format	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.	biomformat	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.	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	98	3906
bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	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.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	240	6736
biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	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.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	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	0	0	0	0	0	0	0
biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	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	1	0	0	1	3
blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	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	1	0	0	78	511
blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	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	1	1	0	24	185
bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	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. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	1	0	0	1	1	0	5136	380252
bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	326	18351
breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	1	1	0	50	1871
brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	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
busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	1804	86180
bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	2	1	2	0	0	2	0	2	0	0	0	2	2	2	5295	981251
bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	0	1220	44386
bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	201	10619
cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234
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.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	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.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	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	8	1393
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								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	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
cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	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.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	5	5	0	268	2878
cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474
cemitool	cemitool	Gene co-expression network analysis tool	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.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	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	1	0	0	9	98
charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589
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	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	10	0	0	390	5165
cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	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.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	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	2	0	0	1	207
chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	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
chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	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	5	5	0	97	6418
chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				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
chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	182	2130
circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	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	1	0	0	16	269
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	galactic_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.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	11	0	0	0	11	11	0	1018	21305
cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	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	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	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	1	0	0	1	18
clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	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.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	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	1	0	0	68	1856
clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	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.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	651	46793
clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	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
cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	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
cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	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
cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	45	370
codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	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	1	1	0	29	60901
cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	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.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757
colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	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	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			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	2	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
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								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	251
collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	1483	20857
collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	1	0	0	0	1	1	0	912	5059
column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	1	0	0	0	1	1	0	2379	3883271
column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	3258
column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	199	8424
compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"Compleasm: a faster and more accurate reimplementation of BUSCO"	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	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
compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	375	35084
compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	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	1	0	0	164	3674
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.	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.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786
cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	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
coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			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
coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	72	529
crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	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.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	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	1	1	0	30	636
crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	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	1	1	0	17	347
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								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	6	5	0	116	1968
cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	1	1	0	65	1130
cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	1	0	228	5831
cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	1	1	0	0	1	1	0	319	32218
cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	1	0	122	3292
cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	27	660
cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	18	688
cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	5090	232004
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.	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	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	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	1	0	0	17	235
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.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				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
dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	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.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	10	10	0	1263	66609
das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	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.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706
data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	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.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	1	0	0	0	3	3	0	3066	739298
decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	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	1	0	0	15	99
deepmicro	deepmicro	Representation learning and classification framework	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.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	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	1	0	0	3	501
deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	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	5
deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	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	1	0	0	182	1889
deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	1774	19910
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.	delly2	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.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.8	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	6	0	0	0	6	0	0	124	1135
deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	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.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	4990	95752
dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	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.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	218	16064
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.	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.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	3	3	0	963	49711
diffbind	diffbind	Diffbind provides functions for processing ChIP-Seq data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	6264
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.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	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	0	0	0	0	0	0
disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	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.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	42	369
dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	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
dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			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
dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886
drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	46	646
dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	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.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	126	3934
ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	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	1	1	0	52	382
edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	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.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	1	0	0	0	1	1	0	945	18117
egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	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	1	1	0	177	2524
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	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	107	0	0	0	107	107	0	1816	89530
ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA).								Up-to-date	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	14	208
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								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	5	5	0	126	2257
ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	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	1	0	0	119	2653
episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	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	3	0	0	20	736
evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	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.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	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.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	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	1	1	0	29	410
exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	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.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	59	988
export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	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.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	200	5265
extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	0	0	0	1	0	0	0	1	1	0	285	11846
falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.3	falco	1.2.3	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	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
fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	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.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	52	459
fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	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	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	242	2644
fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0
fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	1	1	1	68	2912
fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	29	774
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.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	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	1	1	0	15	160
fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	1080	35336
fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	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.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	250	3498
fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	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
fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	1	2803	1055760
fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	66	8676
fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	266	14222
fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	1028	94802
fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	69	2503
fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/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	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	170
fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/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	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	122	8410
fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/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	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	1087	17024
fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/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	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	245	16635
fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/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	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	196	3092
fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	51	1178
fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	11	220
fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	1	1	0	1509	15172
fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	221	4246
fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	1	1	0	419	13599
fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	93	12593
fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	210	9757
fastqc	fastqc	Read QC reports using FastQC	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. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	1	1	1	1	0	17447	1556625
fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	1	1	0	1266	4333
fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	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	1	1	0	1371	178178
fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	379	55434
fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	27	1810
fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	128	16591
fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	96	3333
fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	114	61218
fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	25	249
fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	63	2176
fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	68	2280
fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	156	10832
fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	205	13149
fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	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	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	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	1	0	0	22	285
featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	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. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	4679	696399
feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	1191
fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	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	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.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	307	5240
filtlong	filtlong	Filtlong - Filtering long reads by quality	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.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	617	30483
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.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	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	2	0	0	14	331
flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	74	13759
fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	68	1102
freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	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.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	2	0	0	0	2	2	0	3059	155087
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.	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.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	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	1	1	0	44	665
freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	4	0	0	55	20021
fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	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
funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	900	5906
gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	1	1	0	181	2483
gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	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
gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	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	1	0	0	112	519
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	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.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	662	4916
genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	1	1	1	1	1	0	1	1	0	0	1	0	0	1	1	1	0	1	0	0	0	1	0	0	1	1	1	0	1	4
genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	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.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	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	1	0	0	5	67
genetrack	genetrack	Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				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
genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	329	2118
genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	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	1	0	0	11	46
genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	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	1	1	0	79	3515
get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	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	1	0	0	1	4
getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	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.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	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	2	0	0	18	495
gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	332	8274
gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	135
gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	381	3477
gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	680	10995
ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	3	0	0	0	5	5	0	1388	22148
ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-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
glimmer	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.	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.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	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	4	0	0	187	3965
goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	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 Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	408	5484
goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	1	1	0	1210	19167
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								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	196	3443
graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	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	1	1	0	2	63
graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	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.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	432	9277
gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	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.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	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
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.	GTDB-Tk	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).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	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
gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	1	1	0	1200	8107
gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	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	1	1	0	145	3340
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.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	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	0	0	0	0	0	0	0
gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	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
hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	117	4459
hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	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.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	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	1	1	0	18	339
hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	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	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		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
hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	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.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295
happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	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.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	1953	44240
heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	242	1186
hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	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
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_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.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	36	33	0	1085	66003
hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	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	0	0	0	0	0	0
hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	297	1410
hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	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.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	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	1	0	0	12	137
hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	1	1	0	4183	299104
hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.6.8			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	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).	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.	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	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	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	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	12	12	0	439	33702
homer	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.	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.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	5	0	0	394	6937
htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	1	0	0	0	1	1	0	1419	154533
humann	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	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)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	To update	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	13	13	13	6	13	13	13	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	13	13	0	1045	19521
hybpiper	hybpiper	Analyse targeted sequence capture data	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.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	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
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, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	17	12	0	161	10370
hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	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.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	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	1	0	0	39	354
icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	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
idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	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.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127
idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	30	2873
idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.44.1	omero-py	5.11.1			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	361
iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	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	1	1	0	12	1506
infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	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
instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	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	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	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	2	0	0	5	94
integron_finder	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"	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	58	52965
intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	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	1	1	0	1	44
interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	677	35243
interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	1	1	0	5	105
intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	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.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	1497
iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	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	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	681	21598
irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	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	1	1	0	4	29
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."	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	50	57581
isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	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.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822
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								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	4	0	0	0	5	5	0	1171	1224275
iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	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.	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	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	3	3	0	3	542
jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	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	1	1	0	3	30
jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	2	0	0	0	2	2	0	2346	18229
jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	2469
jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	91	1138
join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			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
jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	21	2312
jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	249	6285
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.	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.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.0	Gene expression profiling	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	2	2	0	299	24155
kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	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	1	1	0	19	363
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	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.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	8	8	0	63	2022
king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	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	1	0	0	3	5
kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	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).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	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	1	0	0	38	319
kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	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	1	1	0	0	0
kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	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.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	33	594
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.	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.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	5	5	0	1209	33778
kraken2	kraken2	Kraken2 for taxonomic designation.	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.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	1	1	1	0	2367	185308
kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444
kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	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	1	1	0	354	2527
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	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	6	0	0	703	16525
krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	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
last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	41	227
lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	2	2	0	188	83331
lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	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.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	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	1	0	0	7	55
length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	1	1	0	322	4090
limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1012	20344
lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	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).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	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	1	0	0	2	37
links	links	Scaffold genome assemblies with long reads.	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.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	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	1	0	0	77	405
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. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	4	5	5	5	4	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	4	0	0	0	5	5	0	1791	4150903
lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	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	1	0	0	9	647
lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	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	2	0	0	105	1164
m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	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	3
maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	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.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	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	1	0	0	29	188
macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	9	0	0	0	9	9	0	1969	84521
maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	1	1	1	1	1	0	1	1	0	0	1	0	0	1	1	1	0	1	0	0	0	1	0	0	1	1	1	0	3	21
maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	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	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	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
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.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	5	5	0	587	10503
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.	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.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	2	0	554	5591
malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	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	1	0	0	6	22
map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	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	9	1528
mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	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	1	0	0	2	167
mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	27	9763
mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	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
masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	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.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	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	1	1	0	13	576
maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	118	2059
mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	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	1	1	0	10	29
medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	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.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	2	0	0	0	3	3	0	768	99863
megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	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.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	1	1	1	0	548	9530
megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	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.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	54	475
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).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) 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.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610
meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	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.	meme_meme	meme_meme, meme_fimo		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	4	4	0	235	22352
meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	287	6584
meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	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	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	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, 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
merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	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.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483
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.	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.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence 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
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.	MetaBAT_2	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	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	2	0	0	192	4329
metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	Up-to-date	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.5	Taxonomic classification	Taxonomy	0	0	0	0	0	0	0	0	0	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.	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	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	1	1	0	16	184
metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	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.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	6	753
metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	4	4	0	499	11069
metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	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.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	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
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.	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.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	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
microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	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
migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	7	1226
minia	minia	Short-read assembler based on a de Bruijn graph	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.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	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	1	1	0	109	2206
miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	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.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	178	11938
minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	1	0	0	0	1	1	0	1588	260442
miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	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.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842
mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	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
mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	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	1	0	0	4	10
mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	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	1	0	0	66	881
mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	1	0	236	100920
mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	635	9304
moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	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	1	1	0	19	317
mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	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	1	0	0	21	262
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	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	129	129	0	14353	302916
msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	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	1	1	0	34	803
multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				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
multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	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.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	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	1	0	0	2	53
multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	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. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	8320	162790
mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	6	6	0	669	18347
mykrobe	mykrobe_predict	Antibiotic resistance predictions	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	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	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	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	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	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	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	0	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	3
naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	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	0	0	0	0	0	0	0
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.	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	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	2	0	3	836
nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	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	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	1	1	0	2195	63235
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.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	15	1074
ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	1	0	688	5487
ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	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.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	2	2	0	667	3177
ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0
ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, 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								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	2	0	0	0	8	8	0	169	3193
ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	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.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	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	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	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
necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	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	1	0	0	95	667
newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	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.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	448	25505
nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	1	0	0	0	2	0	0	210	4080
ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	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.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	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	1	0	0	21	1266
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.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	224	24740
nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	5	142
novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	162	6384
nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	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	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.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251
ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	32	1877
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.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	25
omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	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
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.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	4	4	0	39	2654
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.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	22	655
optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	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								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	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	1	0	0	24	321
orfipy	orfipy	Galaxy wrapper for ORFIPY	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.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	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	1	0	0	53	774
orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	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.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	239	1333
packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	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.	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).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	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
pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	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
pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	0	259	7276
parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	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	1	0	0	31	90
pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	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.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	565	5260
pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	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.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	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
pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	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.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	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
pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	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
pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.1	openjdk				1	1	1	1	1	1	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	312	4180
peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	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
pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	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.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	1	1	0	0	150	4305
pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	\n pharokka\n		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	0	74	2565
phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812
phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	104	1770
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.	picard_samtofastq	picard_replacesamheader, picard_samtofastq, picard_reordersam, picard_fastqtosam		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	31	31	31	31	31	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	31	0	0	0	31	31	0	3735	374458
pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	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	1	0	0	2	116
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	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.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	5	5	0	45	1095
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	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.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	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	7	0	0	88	1000
pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	467	7942
pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	83	983
pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	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	1	1	0	16	208
plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	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	1	1	0	278	22589
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"	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22
plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	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.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	669
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."	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.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	24	239
porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	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	1	1	0	1046	185468
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.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	13	13	0	409	18773
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.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	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
pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350
prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	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.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	70	7881
prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	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
progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	286	1734
prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	1	1	1	0	3233	371445
prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	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	1	0	0	5	5
proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	3	3	0	200	3320
psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	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	1	0	0	1	15
pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	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	1	1	0	36	1423
purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	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. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	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	1	0	0	167	16800
pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	350	21123
pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	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	1	1	0	38	2424
pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	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:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	377	11332
pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0	0	26	144
qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	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_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_core, qiime_add_on		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909
qiime_core	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	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	31	31	0	1155	28681
qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	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
qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			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
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.	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.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	1	0	0	0	4	4	0	1328	664470
quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	1	0	3567	51567
query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	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	1
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								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	1	3	3	3	1	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	1	0	0	0	3	3	0	561	124536
quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	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.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	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
raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	82	4569
ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	237	2833
rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	14	176
rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	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
raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	262	6902
raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	383	6808
rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	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.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	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	1	1	0	30	569
read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	71	3370
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."	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.1	recentrifuge	1.14.1	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	48	331
red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	88	578
repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	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).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	248	3750
repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	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.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	217	1177
repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				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
reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	33	3456
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.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	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	1	1	0	5	85
revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	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
rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	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	1	0	0	3	44
rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	2	0	0	0	2	2	0	4015	425658
ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	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	2	0	0	14	161
rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110
roary	roary	Roary the pangenome pipeline	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.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	656	12225
rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	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
rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	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
rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	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
rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	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
rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	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
rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	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
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	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.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	22	0	0	0	22	22	0	3206	133498
ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	76	1236
salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	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	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	84	454
samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, 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
samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			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	0	0	0	0	0	0
sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	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	1	0	0	18	123
sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	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	1	1	0	7	173
sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	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	1	1	0	1	140
sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	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
scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	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.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	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	6	6	0	766	51978
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.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	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	5	5	0	77	1365
sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	90	721
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.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	0	23	779
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								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			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	1
scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	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.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	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	1	0	0	61	676
scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	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.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	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	1	1	0	11	628
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.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	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	1	1	0	50	3647
selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	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
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	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542
seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	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.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	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	1	1	0	16	288
seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	16	68
seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	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.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	2	0	2	5	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	3	0	0	129	1964
seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	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
seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	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)	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	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	12
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	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.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	15	0	0	0	14	14	14	753	59668
seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	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	1	1	0	0	271
seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	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
shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	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	1	0	0	154	763
shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	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.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	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
shovill	shovill	Faster de novo assembly pipeline based around Spades	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.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1008	41600
sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	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.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	269	14982
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.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	34	142
sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	42	1128
sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								To update	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.9.0	sinto	0.10.1			2	2	2	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	2	0	0	17	91
slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	361
sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	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	1	0	0	8	64
smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	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	1	0	0	6	121
smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	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	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	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	1	1	0	22	203
snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	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	1	1	0	133	1349
snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	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
sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	To update	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	1.0.12	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	58	919
snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0	0	22	669
snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	3	2	0	1372	105708
snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	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	1	1	0	367	4558
snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	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	1	1	0	284	5107
snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	5	5	5	5	5	0	0	0	0	0	0	1	0	0	0	5	5	0	0	5	0	5	0	0	0	5	5	0	2676	95592
snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	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).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	1	0	533	760352
snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	0	156	3530
snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	8	8	8	8	8	0	0	0	0	0	0	8	0	0	0	0	8	0	0	8	0	8	0	0	0	8	8	0	1352	5114712
snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	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	1	1	0	11	46
snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	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	1	1	0	31	528
socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	13	621
sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	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	1	0	0	1	1
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.	spades	spades, biosyntheticspades, rnaviralspades, plasmidspades, rnaspades, metaviralspades, metaspades, coronaspades, metaplasmidspades		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.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	3	0	0	0	9	3	0	3547	72953
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.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	0	34	446
spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			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
spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	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	1	0	0	12	1278
spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	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	1	0	0	1	67
sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	3	0	0	0	3	3	0	6247	350032
srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	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	1	0	0	22	205
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	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.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	152	11635
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								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292
star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	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	1	1	0	35	1212
straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	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	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.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	53	549
stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	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.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	0	2165	167659
structure	structure	for using multi-locus genotype data to investigate population structure.	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.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	2623
structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	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.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	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	1	0	0	2	30
table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	741	208652
tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	7388
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.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	7	164
tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	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
taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	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
taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			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
taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	1	1	1	0	1801	27426
taxpasta	taxpasta	standardise taxonomic profiles	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.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	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
tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	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	1	1	0	198	5161
tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	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	1	1	0	209	19252
tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584
tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	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	1	1	0	167	2290
te_finder	te_finder	Transposable element insertions finder	tefinder	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.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	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	1	0	0	7	81
telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	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.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence 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
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.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	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	1	1	0	33	871
tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	8	69
tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								To update	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.6	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	4	0	0	17	1881
tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	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.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9	tooldistillator	0.9	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	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
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.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	1	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
tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	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	4	0	0	58	2439
transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	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.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	348	5468
transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	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.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	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	5	5	0	84	907
transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	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	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	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	1	1	0	5	229
trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	1	1	1	1	0	5862	305866
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	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.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	11	1	0	0	13	12	0	1762	31951
trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	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	1	1	0	151	1796
trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	5	0	0	147	8942
tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	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.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	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	5
tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	368
twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	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	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	48	502
tximport	tximport	Wrapper for the Bioconductor package tximport	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.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	To update	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.22.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	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	1	1	0	88	1408
ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	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
ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	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
ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	To update	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	377	ucsc-blat	469	Sequence alignment	Sequence 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	1	0	0	0	0	0	0	0	0
ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	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	469	ucsc-chainnet	469		Sequence analysis	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
ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	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
ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	455	ucsc-chainsort	469		Sequence analysis	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
ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	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
ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	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
ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	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
umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	5	0	0	0	5	5	0	379	61618
unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	1	0	0	0	1	1	0	1558	65732
usher	usher_matutils, usher	UShER toolkit wrappers	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.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	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	2	0	0	5	1060
valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	20	637
vapor	vapor	Classify Influenza samples from raw short read sequence data	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.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	94	3164
vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	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	1	1	1	16	273
variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	3	88
varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	3	3	0	492	9779
varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	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.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	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
vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	29	751
vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	352	167913
vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	8	357
vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	286	15803
vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	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	1	0	0	87	872
vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	77	2181
vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	28	192
vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	80	3217
vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	13	471
vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	39	675
vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	99	1695
vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	14	244
vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	40	564
vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	882	44437
vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	71	917
vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	6	177
vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	36	718
vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	48	451
vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	90	1370
vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	10	279
vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	12	708
vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	5	159
vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	29	854
vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	63	1852
vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	1	0	265	972774
vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	3	3	0	74	2020
velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	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	1	0	0	0	2
velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420
velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	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.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	1	1	0	255	4741
verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	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	1	0	0	9	22
vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	3	477
virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	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.	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	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
virheat	virheat	generates a heatmap of allele frequencies from vcf files	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.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	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
virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	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).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	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	1	0	0	40	234
volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	1	1	0	1749	30946
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.	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.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	8	0	0	0	8	8	0	182	8507
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.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	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	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	0	74	2379
wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	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
windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	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	85
winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	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	1	0	0	27	248
xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	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	1	1	0	3	234
yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	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	1	0	0	64	344
zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	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	1	1	0	2	90
EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, 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								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	9	9	0	0	9	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102
Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82
Geom_mean_workflow	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).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	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	0.1.0+galaxy0	r-base				0	0	3	3	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
PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004
ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	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	1	1	0	34	2689
ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	175	40271
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.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	7	5	0	243	40666
appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	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
aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	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
artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	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	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	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	3	0	0	3	11
bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	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
baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	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								To update		Proteomics	bed_to_protein_map	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	0.2.0	python				1	1	1	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	1	1	0	49	385
bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	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	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	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	3+galaxy0	ucsc-bigwiginfo	469			0	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
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.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	5	5	0	510	8913
biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	53	459
biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	1	0	1	1	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
blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	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	101	1232
blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	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	2.6.0	blast	2.16.0			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
blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	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	1	1	0	121	22499
blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	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	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0
blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				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
blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	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	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0
blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	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	1.1.1	python				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
blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	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	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	159	264558
bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348
c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.2.0	python				1	1	1	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	1	0	0	5	198
cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	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	1	0	0	1	52
calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	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	1	0	0	0	0
cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	1	0	0	101	7766
cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, 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								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	11	9	0	277	48705
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.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	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	2	0	0	16	217
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								To update		Transcriptomics, RNA, Statistics	suite_cell_types_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/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	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	2	6
cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	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	1	0	0	1	13
champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174
checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	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.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, 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
cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	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	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	1	0	0	0	0	0	0	0	0
climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	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	1	1	0	23	237
concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	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	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	352	3612
consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	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	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	55	585
consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			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
cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11	81
cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	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	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0
cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	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+galaxy0	unzip				0	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
custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	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	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	1652
custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	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
data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	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	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	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	1	1	0	34	439
data-scxa	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								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	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	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799
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								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658
data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	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
data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	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
dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	161	4758
decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	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	1.4.0+galaxy3	decoupler	1.5.0			0	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	6
decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	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
deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			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	0	0	0	0	0	0	0
dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	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	1	1	0	2	33
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.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	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	1	0	0	1	40
diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	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	1	0	0	3	15
diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	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	1	1	0	11	245
diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	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	1	0	0	5	7
digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	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										To update			directag_and_tagrecon	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
dose_responses	dr_curve	A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	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								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	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	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	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	95	973
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								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	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	1.0.4	dropletutils-scripts	0.0.5			2	2	2	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	2	0	0	201	1599
eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	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.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	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	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	1	0	510	30565
embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	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
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								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706
eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	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	1	0	0	4	45
essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	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	0.2.0	python				0	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	1	1	0	15	331
ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	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	1	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								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	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	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	461	29886
fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	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	2	0	0	1	28
fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	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	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	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_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	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	0.4.4	atlas-fastq-provider	0.4.7			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	0	0	0	0	0	0
fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	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	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	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								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	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	0.25.1+galaxy0	fastq_utils	0.25.2			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
fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	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	1	0	0	12	261
feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	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	1	0	0	1	18
fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	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	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0
filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	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	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	426	26274
filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	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								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			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
filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			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
filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			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
find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			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
fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	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	1	1	0	17	645
fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	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
free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	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
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	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	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
fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	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								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	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	0.2.8	garnett-cli	0.0.5			0	0	7	0	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	3	27
gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			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
gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	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
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.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475
genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	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.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	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
getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	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	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0
gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	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	0.2.1	python				1	1	1	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	1	1	0	131	2115
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.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	15	9	0	1442	177844
gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	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	4.3.1+galaxy0	r-optparse	1.3.2			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
gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	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	4.3.1+galaxy0	r-optparse	1.3.2			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
gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	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	4.3.1+galaxy0	r-optparse	1.3.2			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
gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	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	4.3.1+galaxy0	r-optparse	1.3.2			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
gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_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	4.3+galaxy0	r-optparse	1.3.2			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
gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	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	4.1.3+galaxy0	r-optparse	1.3.2			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
gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	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	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	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	1	0	0	14	78
gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	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	2.3.9+galaxy0	r-optparse	1.3.2			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
gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	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	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	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	1	1	0	155	1678
guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					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
hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	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	2	2	0	2	111
hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	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
high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	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	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	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/.								To update	https://github.com/AquaINFRA/galaxy	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	0.2.0	r-base				0	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
hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	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	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	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								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	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	1	1	0	4	275
incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	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	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	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								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	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
isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	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
justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	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
justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0
lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	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	1.0	bioconductor-msnbase	2.28.1			0	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	1	1	0	3	111
longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					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
ltq_iquant_cli										To update			ltq_iquant_cli	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
lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			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	0	0	0	0	0	0
lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	2	2	0	25	3797
manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	8	93
map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	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	0.2	biopython	1.70			0	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	1	1	0	1	41
mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	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	0.22.0	r-optparse	1.3.2			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
marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	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
matchms	matchms_add_key, matchms_convert, 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.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	11	2	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	10	187
maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	2	0	415	6078
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								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	10	10	0	139	3115
mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	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	1	1	0	98	26427
mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	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	1	1	0	9	158
mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	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	1	0	0	3	36
mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	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	0.2.0	python				0	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	1	1	0	0	24
measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	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								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	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
meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	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	2.0.0	mpa-portable	2.0.0			0	0	1	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	1	0	0	10	123
metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	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	1	1	0	115	636
metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	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	1	0	0	15	4181
metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	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.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	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	6	6	0	104	2522
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	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.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	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
mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	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.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	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
misc	use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0					0	1	1	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
moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	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	1	1	0	3	759
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.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	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	0.1.4	monocle3-cli	0.0.9			9	0	9	0	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	264	3266
morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	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	1	1	0	4	140
mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	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	2	0	0	0	2
ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	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.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	Up-to-date	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.0.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	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	0	0	0	0	0
msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	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.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	19958
msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	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	1	1	0	5	507
msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	103
msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110
msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	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	0	0	0	0	0	0	0
msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	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	1	1	0	144	2036
msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	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	1	0	0	71	726
mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	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	1	1	0	19	270
mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			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	0	0	0	0	0
mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	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	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	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	1	1	0	33	844
mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	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+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	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	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	16	0	0	16	16	15	0	4066	365597
oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0
obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	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	6
ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	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
ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	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
omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	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_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								To update		Imaging	omero_clean_rois_tables	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	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	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								To update		Imaging	omero_get_children_ids	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	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	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								To update		Imaging	omero_get_full_images	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	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	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								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	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	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	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								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	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	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	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	1	0	0	25	347
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								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	141	124	0	886	105432
packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	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	1	1	0	15	288
pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	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	1	0	0	10	228
pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	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	1	1	0	20	238
pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	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	1	1	0	9	498
pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	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	1	1	0	23	4862
pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	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	717
peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	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	1	1	0	9	468
peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.9			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	0	485	17477
pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	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
percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	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	4	4	0	5	368
pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	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.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	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
pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	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.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			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
positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			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
probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	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
proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	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	proteomiqon-joinquantpepionswithproteins	0.0.2			0	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	1	0	0	4	366
proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	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	proteomiqon-labeledproteinquantification	0.0.3			0	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	1	0	0	5	14
proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	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	proteomiqon-labelfreeproteinquantification	0.0.3			0	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	1	0	0	3	6
proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	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	1	0	0	5	721
proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	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	1	0	0	6	96
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.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	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	1	0	0	4	686
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.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	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	1	0	0	4	89
proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	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	1	0	0	4	604
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.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	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	1	0	0	4	694
proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	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
protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	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
psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_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
psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	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	1	0	0	0	20
psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.2.1	python				0	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	1	1	0	46	469
pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	33	2509
pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	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	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.3	Protein identification	Proteomics, Proteomics experiment	0	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	1	0	0	2	81
pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	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	0.10.0	astropy				0	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	1	0	0	4	36
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).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	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
quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230
quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	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	1	1	0	1	32
query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	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								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	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	1	0	0	5	59
ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	16
rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	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	1	1	0	14	175
rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	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
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.	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.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	7	296
recetox_msfinder	recetox_msfinder		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.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	1	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
recetox_xmsannotator	recetox_xmsannotator_advanced		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.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	1	0	1	1	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
regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	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	1.0.3	python				2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	2	0	0	0	2	2	0	495	60307
regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	22	526
rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	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
rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	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
repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	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	0	0
repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					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	0	0	0	0	0	0
retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		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.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	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								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	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
retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	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	0.1.0					0	0	0	0	0	0	0	0	0	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.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	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	1	0	0	9	39
riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	1	1	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	1	0	1	1	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
rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	1	1	0	67	377
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								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	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	0.0.1+galaxy6	scipy				1	1	1	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	86	561
sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				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
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.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	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	1.8.0	sc3-scripts	0.0.6			0	0	7	0	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	1	9
scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	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
scanpy	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.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	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	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356
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.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	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	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	16	387
sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	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	0.0.9	sccaf	0.0.10			4	3	4	0	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	2	110
sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	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	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	90	721
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.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	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	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	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	83
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								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	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	1.0.2	scpred-cli	0.1.0			0	0	4	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	4	25
scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	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.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	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
sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	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	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0
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								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	181	1966
sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	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+galaxy0	ipython				0	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
shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	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	1	1	0	2	63
sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	4	4	0	24	293
small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	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	1.3.0	pysam	0.22.1			0	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
small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	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	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	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.								To update	http://artbio.fr	RNA	small_rna_signatures	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	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	2	0	0	0	0	0	0	0	0
smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	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								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			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
snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			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
spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	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.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	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
spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			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
spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			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
spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	56	769
sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0
sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	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	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	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								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225
stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325
suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	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
tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	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	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	8	50
translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	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	0.1.0					1	1	1	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	1	1	0	49	643
translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	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	0.2.0	biopython	1.70			0	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	1	1	0	6	57
ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	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	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	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	1	1	0	78	941
unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	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	1	1	0	115	5005
uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	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	1	1	0	79	1360
upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	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	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	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.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	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	1	0	0	25	86
varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	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								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			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
verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			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
vibrant	vibrant	Virus Identification By iteRative ANnoTation	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	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203
virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
vmd		vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	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
waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	1	1	1	1	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	6
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.								To update	http://xarray.pydata.org	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	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876
xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	14
xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	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	0	0	0	0	0	0	0
xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	1	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
yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	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								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	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	2.0.4	shapely				0	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
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.								To update	https://github.com/AquaINFRA/galaxy	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	0.1.0	r-base				0	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