Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Date of first commit of the suite	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 UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers
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	2023-11-07	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	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11
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	2024-08-12	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	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12
chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing							To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	2023-01-18	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	14	14	6	6	0	0	0	0	14	14	6	6
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	2023-01-09	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	1	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28
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	2023-03-16	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	1	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7
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	2024-08-12	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	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2
flux	black_forest_labs_flux	Using the black forest labs FLUX.1 models to generate image based on user input.							To update	https://github.com/bgruening/galaxytools/tree/master/tools/cflux	Machine Learning	black_forest_labs_flux	2024-10-14	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flux	https://github.com/bgruening/galaxytools/tree/master/tools/flux	2024	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
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	2021-04-12	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	29	31	27	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362
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	2019-08-23	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	1	1	1	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57
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	2022-09-13	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	1	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76
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	2024-04-23	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	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13