Expand	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 CIRM-CFBP	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 ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	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)	Deprecated
	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	0	0	0	0	0	13
	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	0	0	0	0	0
	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	0	0	0	0	0
	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	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	0	0	0	0	0	1	0	0	3	501
	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	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	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	0	0	0	0	0	31	27	0	958	113932
	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	0	0	0	0	0	1	1	0	15	445
	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	0	0	0	0	0	1	0	0	40	234
	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	0	0	0	0	0