diff --git a/README.md b/README.md index 992a829f..2d19b61d 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,43 @@ Galaxy Codex Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools, training, workflows) that can be filtered for any community. -This repository stores the sources to build this catalog. The catalog is automatically updated every week. - +This repository stores the sources to build this catalog and its content. The catalog is automatically updated every week. Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN tutorial**. + +# Catalog content + +## Tool table + +Column | Description +--- | --- +Suite ID | ID of Galaxy suite +Tool IDs | List of Galaxy tool IDs +Description | Description of the suite +Homepage | Homepage for tool +Suite version | Version of the Galaxy suite +Suite Conda package | Conda package used as requirement for the suite +Latest suite conda package version | Latest Conda package version on anaconda +Suite version status | Update status derived by comparing the suite version to the latest conda package version +ToolShed categories | +EDAM operations | EDAM operations extracted using bio.tools +EDAM reduced operations | EDAM operations where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed +EDAM topics | EDAM topics extracted using bio.tools +EDAM reduced topics | EDAM topics where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed +Suite owner | Owner of the Galaxy suite +Suite source | Path to the Galaxy suite +bio.tools ID | ID of the bio.tools entry corresponding to the tool +bio.tools name | Name of the bio.tools entry corresponding to the tool +bio.tools description | Description in bio.tools entry corresponding to the tool +bii ID | ID of BII entry corresponding to the tool +Number of tools available on ... | Number of tools available on given Galaxy server +Suite users (last 5 years) on ... | Number of users of the suite in the last 5 years on given Galaxy server +Suite users on ... | Number of users of the suite on given Galaxy server +Suite runs (last 5 years) on ... | Number of runs of the suite tools in the last 5 years on given Galaxy server +Suite runs on ... | Number of runs of the suite tools on given Galaxy server +Suite users (last 5 years) on main servers | Number of users of the suite in the last 5 years on all UseGalaxy servers +Suite users on main servers | Number of users of the suite on all UseGalaxy servers +Suite runs (last 5 years) on main servers | Number of runs of the suite tools in the last 5 years on all UseGalaxy servers +Suite runs on main servers | Number of runs of the suite tools on all UseGalaxy servers +Deprecated | Deprecation status after review by a domain expert +To keep | Status to add to a community after review by a domain expert \ No newline at end of file diff --git a/communities/all/resources/test_tools.json b/communities/all/resources/test_tools.json index 0bad9a6f..c580a197 100644 --- a/communities/all/resources/test_tools.json +++ b/communities/all/resources/test_tools.json @@ -1,391 +1,361 @@ [ { - "Galaxy wrapper id": "2d_auto_threshold", - "Galaxy tool ids": [ + "Suite ID": "2d_auto_threshold", + "Tool IDs": [ "ip_threshold" ], "Description": "Automatic thresholding", - "bio.tool id": "scikit-image", - "bio.tool ids": [ - "scikit-image" + "Suite first commit date": "2024-03-01", + "Homepage": "https://github.com/bmcv", + "Suite version": "0.0.6-2", + "Suite conda package": "scikit-image", + "Latest suite conda package version": null, + "Suite version status": "To update", + "ToolShed categories": [ + "Imaging" ], - "biii": "scikit-image", - "bio.tool name": "scikit-image", - "bio.tool description": "Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.", - "EDAM operation": [ + "EDAM operations": [ "Image analysis", "Image annotation", "Visualisation", "Data handling" ], - "EDAM topic": [ - "Imaging", - "Software engineering", - "Literature and language" - ], - "Status": "To update", - "Source": "https://github.com/bmcv", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "2d_auto_threshold", - "Date of first commit of the suite": "2024-03-01", - "Galaxy wrapper owner": "imgteam", - "Galaxy wrapper source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/", - "Galaxy wrapper parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold", - "Galaxy wrapper version": "0.0.6-2", - "Conda id": "scikit-image", - "Conda version": null, - "EDAM operation (no superclasses)": [ + "EDAM reduced operations": [ "Image analysis", "Image annotation", "Visualisation", "Data handling" ], - "EDAM topic (no superclasses)": [ + "EDAM topics": [ + "Imaging", + "Software engineering", + "Literature and language" + ], + "EDAM reduced topics": [ "Imaging", "Software engineering", "Literature and language" ], - "Available on UseGalaxy.org (Main)": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.fr": 0, - "Tools available on UseGalaxy.org (Main)": 0, - "Tools available on UseGalaxy.org.au": 1, - "Tools available on UseGalaxy.eu": 1, - "Tools available on UseGalaxy.fr": 0, - "Tools available on APOSTL": 0, - "Tools available on BF2I-MAP": 0, - "Tools available on BioBix": 0, - "Tools available on CIRM-CFBP": 0, - "Tools available on Center for Phage Technology (CPT)": 0, - "Tools available on ChemFlow": 0, - "Tools available on Coloc-stats": 0, - "Tools available on CoralSNP": 0, - "Tools available on CropGalaxy": 0, - "Tools available on Dintor": 0, - "Tools available on FreeBioinfo": 0, - "Tools available on GASLINI": 0, - "Tools available on Galaxy@AuBi": 0, - "Tools available on Galaxy@Pasteur": 0, - "Tools available on GalaxyTrakr": 0, - "Tools available on Genomic Hyperbrowser": 0, - "Tools available on GigaGalaxy": 0, - "Tools available on HyPhy HIV NGS Tools": 0, - "Tools available on IPK Galaxy Blast Suite": 0, - "Tools available on ImmPort Galaxy": 0, - "Tools available on InteractoMIX": 0, - "Tools available on MISSISSIPPI": 0, - "Tools available on Mandoiu Lab": 0, - "Tools available on MiModD NacreousMap": 0, - "Tools available on Oqtans": 0, - "Tools available on Palfinder": 0, - "Tools available on PepSimili": 0, - "Tools available on PhagePromotor": 0, - "Tools available on UseGalaxy.be": 1, - "Tools available on UseGalaxy.cz": 1, - "Tools available on UseGalaxy.no": 1, - "Tools available on Viral Variant Visualizer (VVV)": 0, - "No. of tool users (5 years) (usegalaxy.eu)": 1434, - "No. of tool users (all time) (usegalaxy.eu)": 6746, - "Tool usage (5 years) (usegalaxy.eu)": 120, - "Tool usage (all time) (usegalaxy.eu)": 122, - "No. of tool users (5 years) (usegalaxy.org)": 0, - "No. of tool users (all time) (usegalaxy.org)": 0, - "Tool usage (5 years) (usegalaxy.org)": 0, - "Tool usage (all time) (usegalaxy.org)": 0, - "No. of tool users (5 years) (usegalaxy.org.au)": 305, - "No. of tool users (all time) (usegalaxy.org.au)": 305, - "Tool usage (5 years) (usegalaxy.org.au)": 11, - "Tool usage (all time) (usegalaxy.org.au)": 11, - "No. of tool users (5 years) - all main servers": 1739, - "No. of tool users (all time) - all main servers": 7051, - "Tool usage (5 years) - all main servers": 131, - "Tool usage (all time) - all main servers": 133 + "Suite owner": "imgteam", + "Suite source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/", + "Suite parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold", + "bio.tool ID": "scikit-image", + "bio.tool name": "scikit-image", + "bio.tool description": "Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.", + "biii ID": "scikit-image", + "Number of tools on UseGalaxy.org (Main)": 1, + "Number of tools on UseGalaxy.org.au": 1, + "Number of tools on UseGalaxy.eu": 1, + "Number of tools on UseGalaxy.fr": 1, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 0, + "Number of tools on Galaxy@Pasteur": 0, + "Number of tools on GalaxyTrakr": 0, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on IPK Galaxy Blast Suite": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on MISSISSIPPI": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MiModD NacreousMap": 0, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PepSimili": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 1, + "Number of tools on UseGalaxy.cz": 1, + "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 120, + "Suite users (usegalaxy.eu)": 122, + "Suite runs (last 5 years) (usegalaxy.eu)": 1434, + "Suite runs (usegalaxy.eu)": 6746, + "Suite users (last 5 years) (usegalaxy.org)": 0, + "Suite users (usegalaxy.org)": 0, + "Suite runs (last 5 years) (usegalaxy.org)": 0, + "Suite runs (usegalaxy.org)": 0, + "Suite users (last 5 years) (usegalaxy.org.au)": 11, + "Suite users (usegalaxy.org.au)": 11, + "Suite runs (last 5 years) (usegalaxy.org.au)": 305, + "Suite runs (usegalaxy.org.au)": 305, + "Suite users (last 5 years) on main servers": 131, + "Suite users on main servers": 395, + "Suite runs (last 5 years) on main servers": 1739, + "Suite runs on main servers": 10529 }, { - "Galaxy wrapper id": "abritamr", - "Galaxy tool ids": [ + "Suite ID": "abritamr", + "Tool IDs": [ "abritamr" ], "Description": "A pipeline for running AMRfinderPlus and collating results into functional classes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://zenodo.org/record/7370628", + "Suite first commit date": "2024-03-01", + "Homepage": "https://zenodo.org/record/7370628", + "Suite version": "1.0.14", + "Suite conda package": "abritamr", + "Latest suite conda package version": "1.0.19", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], - "ToolShed id": "abritamr", - "Date of first commit of the suite": "2024-03-01", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", - "Galaxy wrapper parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr", - "Galaxy wrapper version": "1.0.14", - "Conda id": "abritamr", - "Conda version": "1.0.19", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org (Main)": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.fr": 0, - "Tools available on UseGalaxy.org (Main)": 0, - "Tools available on UseGalaxy.org.au": 0, - "Tools available on UseGalaxy.eu": 1, - "Tools available on UseGalaxy.fr": 0, - "Tools available on APOSTL": 0, - "Tools available on BF2I-MAP": 0, - "Tools available on BioBix": 0, - "Tools available on CIRM-CFBP": 0, - "Tools available on Center for Phage Technology (CPT)": 0, - "Tools available on ChemFlow": 0, - "Tools available on Coloc-stats": 0, - "Tools available on CoralSNP": 0, - "Tools available on CropGalaxy": 0, - "Tools available on Dintor": 0, - "Tools available on FreeBioinfo": 0, - "Tools available on GASLINI": 0, - "Tools available on Galaxy@AuBi": 0, - "Tools available on Galaxy@Pasteur": 0, - "Tools available on GalaxyTrakr": 0, - "Tools available on Genomic Hyperbrowser": 0, - "Tools available on GigaGalaxy": 0, - "Tools available on HyPhy HIV NGS Tools": 0, - "Tools available on IPK Galaxy Blast Suite": 0, - "Tools available on ImmPort Galaxy": 0, - "Tools available on InteractoMIX": 0, - "Tools available on MISSISSIPPI": 0, - "Tools available on Mandoiu Lab": 0, - "Tools available on MiModD NacreousMap": 0, - "Tools available on Oqtans": 0, - "Tools available on Palfinder": 0, - "Tools available on PepSimili": 0, - "Tools available on PhagePromotor": 0, - "Tools available on UseGalaxy.be": 0, - "Tools available on UseGalaxy.cz": 0, - "Tools available on UseGalaxy.no": 0, - "Tools available on Viral Variant Visualizer (VVV)": 0, - "No. of tool users (5 years) (usegalaxy.eu)": 1139, - "No. of tool users (all time) (usegalaxy.eu)": 1139, - "Tool usage (5 years) (usegalaxy.eu)": 109, - "Tool usage (all time) (usegalaxy.eu)": 109, - "No. of tool users (5 years) (usegalaxy.org)": 0, - "No. of tool users (all time) (usegalaxy.org)": 0, - "Tool usage (5 years) (usegalaxy.org)": 0, - "Tool usage (all time) (usegalaxy.org)": 0, - "No. of tool users (5 years) (usegalaxy.org.au)": 0, - "No. of tool users (all time) (usegalaxy.org.au)": 0, - "Tool usage (5 years) (usegalaxy.org.au)": 0, - "Tool usage (all time) (usegalaxy.org.au)": 0, - "No. of tool users (5 years) - all main servers": 1139, - "No. of tool users (all time) - all main servers": 1139, - "Tool usage (5 years) - all main servers": 109, - "Tool usage (all time) - all main servers": 109 + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": "iuc", + "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", + "Suite parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr", + "bio.tool ID": null, + "bio.tool name": null, + "bio.tool description": null, + "biii ID": null, + "Number of tools on UseGalaxy.org (Main)": 0, + "Number of tools on UseGalaxy.org.au": 0, + "Number of tools on UseGalaxy.eu": 1, + "Number of tools on UseGalaxy.fr": 0, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 0, + "Number of tools on Galaxy@Pasteur": 0, + "Number of tools on GalaxyTrakr": 0, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on IPK Galaxy Blast Suite": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on MISSISSIPPI": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MiModD NacreousMap": 0, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PepSimili": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 0, + "Number of tools on UseGalaxy.cz": 0, + "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 109, + "Suite users (usegalaxy.eu)": 109, + "Suite runs (last 5 years) (usegalaxy.eu)": 1139, + "Suite runs (usegalaxy.eu)": 1139, + "Suite users (last 5 years) (usegalaxy.org)": 0, + "Suite users (usegalaxy.org)": 0, + "Suite runs (last 5 years) (usegalaxy.org)": 0, + "Suite runs (usegalaxy.org)": 0, + "Suite users (last 5 years) (usegalaxy.org.au)": 0, + "Suite users (usegalaxy.org.au)": 0, + "Suite runs (last 5 years) (usegalaxy.org.au)": 0, + "Suite runs (usegalaxy.org.au)": 0, + "Suite users (last 5 years) on main servers": 109, + "Suite users on main servers": 327, + "Suite runs (last 5 years) on main servers": 1139, + "Suite runs on main servers": 3417 }, { - "Galaxy wrapper id": "aldex2", - "Galaxy tool ids": [ + "Suite ID": "aldex2", + "Tool IDs": [ "aldex2" ], "Description": "Performs analysis Of differential abundance taking sample variation into account", - "bio.tool id": "aldex2", - "bio.tool ids": [ - "aldex2" + "Suite first commit date": "2024-03-01", + "Homepage": "https://github.com/ggloor/ALDEx_bioc", + "Suite version": "1.26.0", + "Suite conda package": "bioconductor-aldex2", + "Latest suite conda package version": "1.34.0", + "Suite version status": "To update", + "ToolShed categories": [ + "Metagenomics" ], - "biii": null, - "bio.tool name": "ALDEx2", - "bio.tool description": "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.", - "EDAM operation": [ + "EDAM operations": [ + "Statistical inference" + ], + "EDAM reduced operations": [ "Statistical inference" ], - "EDAM topic": [ + "EDAM topics": [ "Gene expression", "Statistics and probability" ], - "Status": "To update", - "Source": "https://github.com/ggloor/ALDEx_bioc", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "aldex2", - "Date of first commit of the suite": "2024-03-01", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", - "Galaxy wrapper parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2", - "Galaxy wrapper version": "1.26.0", - "Conda id": "bioconductor-aldex2", - "Conda version": "1.34.0", - "EDAM operation (no superclasses)": [ - "Statistical inference" - ], - "EDAM topic (no superclasses)": [ + "EDAM reduced topics": [ "Gene expression", "Statistics and probability" ], - "Available on UseGalaxy.org (Main)": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.fr": 0, - "Tools available on UseGalaxy.org (Main)": 0, - "Tools available on UseGalaxy.org.au": 0, - "Tools available on UseGalaxy.eu": 1, - "Tools available on UseGalaxy.fr": 0, - "Tools available on APOSTL": 0, - "Tools available on BF2I-MAP": 0, - "Tools available on BioBix": 0, - "Tools available on CIRM-CFBP": 0, - "Tools available on Center for Phage Technology (CPT)": 0, - "Tools available on ChemFlow": 0, - "Tools available on Coloc-stats": 0, - "Tools available on CoralSNP": 0, - "Tools available on CropGalaxy": 0, - "Tools available on Dintor": 0, - "Tools available on FreeBioinfo": 0, - "Tools available on GASLINI": 0, - "Tools available on Galaxy@AuBi": 0, - "Tools available on Galaxy@Pasteur": 0, - "Tools available on GalaxyTrakr": 0, - "Tools available on Genomic Hyperbrowser": 0, - "Tools available on GigaGalaxy": 0, - "Tools available on HyPhy HIV NGS Tools": 0, - "Tools available on IPK Galaxy Blast Suite": 0, - "Tools available on ImmPort Galaxy": 0, - "Tools available on InteractoMIX": 0, - "Tools available on MISSISSIPPI": 0, - "Tools available on Mandoiu Lab": 0, - "Tools available on MiModD NacreousMap": 0, - "Tools available on Oqtans": 0, - "Tools available on Palfinder": 0, - "Tools available on PepSimili": 0, - "Tools available on PhagePromotor": 0, - "Tools available on UseGalaxy.be": 0, - "Tools available on UseGalaxy.cz": 1, - "Tools available on UseGalaxy.no": 0, - "Tools available on Viral Variant Visualizer (VVV)": 0, - "No. of tool users (5 years) (usegalaxy.eu)": 262, - "No. of tool users (all time) (usegalaxy.eu)": 262, - "Tool usage (5 years) (usegalaxy.eu)": 36, - "Tool usage (all time) (usegalaxy.eu)": 36, - "No. of tool users (5 years) (usegalaxy.org)": 0, - "No. of tool users (all time) (usegalaxy.org)": 0, - "Tool usage (5 years) (usegalaxy.org)": 0, - "Tool usage (all time) (usegalaxy.org)": 0, - "No. of tool users (5 years) (usegalaxy.org.au)": 0, - "No. of tool users (all time) (usegalaxy.org.au)": 0, - "Tool usage (5 years) (usegalaxy.org.au)": 0, - "Tool usage (all time) (usegalaxy.org.au)": 0, - "No. of tool users (5 years) - all main servers": 262, - "No. of tool users (all time) - all main servers": 262, - "Tool usage (5 years) - all main servers": 36, - "Tool usage (all time) - all main servers": 36 + "Suite owner": "iuc", + "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", + "Suite parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2", + "bio.tool ID": "aldex2", + "bio.tool name": "ALDEx2", + "bio.tool description": "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.", + "biii ID": null, + "Number of tools on UseGalaxy.org (Main)": 0, + "Number of tools on UseGalaxy.org.au": 0, + "Number of tools on UseGalaxy.eu": 1, + "Number of tools on UseGalaxy.fr": 0, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 0, + "Number of tools on Galaxy@Pasteur": 0, + "Number of tools on GalaxyTrakr": 0, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on IPK Galaxy Blast Suite": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on MISSISSIPPI": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MiModD NacreousMap": 0, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PepSimili": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 0, + "Number of tools on UseGalaxy.cz": 1, + "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 36, + "Suite users (usegalaxy.eu)": 36, + "Suite runs (last 5 years) (usegalaxy.eu)": 262, + "Suite runs (usegalaxy.eu)": 262, + "Suite users (last 5 years) (usegalaxy.org)": 0, + "Suite users (usegalaxy.org)": 0, + "Suite runs (last 5 years) (usegalaxy.org)": 0, + "Suite runs (usegalaxy.org)": 0, + "Suite users (last 5 years) (usegalaxy.org.au)": 0, + "Suite users (usegalaxy.org.au)": 0, + "Suite runs (last 5 years) (usegalaxy.org.au)": 0, + "Suite runs (usegalaxy.org.au)": 0, + "Suite users (last 5 years) on main servers": 36, + "Suite users on main servers": 108, + "Suite runs (last 5 years) on main servers": 262, + "Suite runs on main servers": 786 }, { - "Galaxy wrapper id": "fastp", - "Galaxy tool ids": [ + "Suite ID": "fastp", + "Tool IDs": [ "fastp" ], "Description": "Fast all-in-one preprocessing for FASTQ files", - "bio.tool id": "fastp", - "bio.tool ids": [ - "fastp" + "Suite first commit date": "2024-03-11", + "Homepage": "https://github.com/OpenGene/fastp", + "Suite version": null, + "Suite conda package": "fastp", + "Latest suite conda package version": "0.23.4", + "Suite version status": "To update", + "ToolShed categories": [ + "Sequence Analysis" ], - "biii": null, - "bio.tool name": "fastp", - "bio.tool description": "A tool designed to provide fast all-in-one preprocessing for FastQ files. 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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.", + "biii ID": null, + "Number of tools on UseGalaxy.org (Main)": 9, + "Number of tools on UseGalaxy.org.au": 9, + "Number of tools on UseGalaxy.eu": 9, + "Number of tools on UseGalaxy.fr": 9, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 1, + "Number of tools on Galaxy@Pasteur": 3, + "Number of tools on GalaxyTrakr": 8, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 2, + "Number of tools on IPK 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(usegalaxy.org.au)": 6653, + "Suite runs (last 5 years) (usegalaxy.org.au)": 54067, + "Suite runs (usegalaxy.org.au)": 61541, + "Suite users (last 5 years) on main servers": 28813, + "Suite users on main servers": 87595, + "Suite runs (last 5 years) on main servers": 257254, + "Suite runs on main servers": 783637 } ] \ No newline at end of file diff --git a/communities/all/resources/test_tools.tsv b/communities/all/resources/test_tools.tsv index f60a80e2..7f68d13f 100644 --- a/communities/all/resources/test_tools.tsv +++ b/communities/all/resources/test_tools.tsv @@ -1,7 +1,6 @@ -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 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 APOSTL Tools available on BF2I-MAP Tools available on BioBix Tools available on CIRM-CFBP Tools available on Center for Phage Technology (CPT) Tools available on ChemFlow Tools available on Coloc-stats Tools available on CoralSNP Tools available on CropGalaxy Tools available on Dintor Tools available on FreeBioinfo 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 PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) 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) -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 2024-03-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold 0.0.6-2 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 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes To update https://zenodo.org/record/7370628 Sequence Analysis abritamr 2024-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr 1.0.14 abritamr 1.0.19 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 -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 2024-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/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 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 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 To update https://github.com/OpenGene/fastp Sequence Analysis fastp 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/fastp fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 -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 metaplasmidspades, rnaspades, metaviralspades, spades, rnaviralspades, plasmidspades, coronaspades, biosyntheticspades, metaspades 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 2024-03-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 0 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 - +Suite ID Tool IDs Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on BF2I-MAP Number of tools on BioBix Number of tools on CIRM-CFBP Number of tools on Center for Phage Technology (CPT) Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CoralSNP Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on GigaGalaxy Number of tools on HyPhy HIV NGS Tools Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on MISSISSIPPI Number of tools on Mandoiu Lab Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) on main servers Suite users on main servers Suite runs (last 5 years) on main servers Suite runs on main servers +2d_auto_threshold ip_threshold Automatic thresholding 2024-03-01 https://github.com/bmcv 0.0.6-2 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 120 122 1434 6746 0 0 0 0 11 11 305 305 131 395 1739 10529 +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes 2024-03-01 https://zenodo.org/record/7370628 1.0.14 abritamr 1.0.19 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 109 109 1139 1139 0 0 0 0 0 0 0 0 109 327 1139 3417 +aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account 2024-03-01 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.34.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 262 262 0 0 0 0 0 0 0 0 36 108 262 786 +fastp fastp Fast all-in-one preprocessing for FASTQ files 2024-03-11 https://github.com/OpenGene/fastp fastp 0.23.4 To update Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 6847 6909 1126086 1127111 10722 10722 422259 422259 2242 2242 76462 76462 19811 59495 1624807 4875446 +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. 2024-03-12 https://github.com/ablab/spades 3.15.5 spades 4.0.0 To update Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 8209 8526 82716 87113 14787 14790 120471 120475 5817 6653 54067 61541 28813 87595 257254 783637 diff --git a/sources/bin/extract_galaxy_tools.py b/sources/bin/extract_galaxy_tools.py index 01279a4c..47a015f4 100644 --- a/sources/bin/extract_galaxy_tools.py +++ b/sources/bin/extract_galaxy_tools.py @@ -40,34 +40,27 @@ public_servers = project_path.joinpath("data", "available_public_servers.csv") -GALAXY_TOOL_STATS = { - # EU - "No. of tool users (5 years) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_usage_5y_until_2024.08.31.csv"), - "No. of tool users (all time) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_usage_until_2024.08.31.csv"), - "Tool usage (5 years) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_users_5y_until_2024.08.31.csv"), - "Tool usage (all time) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_users_until_2024.08.31.csv"), - # ORG - "No. of tool users (5 years) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_usage_5y_until_2024.08.31.csv"), - "No. of tool users (all time) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_usage_until_2024.08.31.csv"), - "Tool usage (5 years) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_users_5y_until_2024.08.31.csv"), - "Tool usage (all time) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_users_until_2024.08.31.csv"), - # AU - "No. of tool users (5 years) (usegalaxy.org.au)": usage_stats_path.joinpath( - "org.au/tool_usage_5y_until_2024.08.31.csv" - ), - "No. of tool users (all time) (usegalaxy.org.au)": usage_stats_path.joinpath( - "org.au/tool_usage_until_2024.08.31.csv" - ), - "Tool usage (5 years) (usegalaxy.org.au)": usage_stats_path.joinpath("org.au/tool_users_5y_until_2024.08.31.csv"), - "Tool usage (all time) (usegalaxy.org.au)": usage_stats_path.joinpath("org.au/tool_users_until_2024.08.31.csv"), -} +GALAXY_TOOL_STATS = {} +for server in ["eu", "org", "org.au"]: + GALAXY_TOOL_STATS[f"Suite users (last 5 years) (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_users_5y_until_2024.08.31.csv" + ) + GALAXY_TOOL_STATS[f"Suite users (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_users_until_2024.08.31.csv" + ) + GALAXY_TOOL_STATS[f"Suite runs (last 5 years) (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_usage_5y_until_2024.08.31.csv" + ) + GALAXY_TOOL_STATS[f"Suite runs (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_usage_until_2024.08.31.csv" + ) # all columns that contain the text will be summed up to a new column with summed up stats GALAXY_TOOL_STATS_SUM = [ - "No. of tool users (5 years)", - "No. of tool users (all time)", - "Tool usage (5 years)", - "Tool usage (all time)", + "Suite users (last 5 years)", + "Suite users", + "Suite runs (last 5 years)", + "Suite runs", ] # load the configs globally @@ -100,15 +93,15 @@ def get_tool_stats_from_stats_file(tool_stats_df: pd.DataFrame, tool_ids: List[s """ # extract tool id - tool_stats_df["Galaxy wrapper id"] = tool_stats_df["tool_name"].apply(get_last_url_position) - # print(tool_stats_df["Galaxy wrapper id"].to_list()) + tool_stats_df["Suite ID"] = tool_stats_df["tool_name"].apply(get_last_url_position) + # print(tool_stats_df["Suite ID"].to_list()) agg_count = 0 for tool_id in tool_ids: - if tool_id in tool_stats_df["Galaxy wrapper id"].to_list(): + if tool_id in tool_stats_df["Suite ID"].to_list(): # get stats of the tool for all versions - counts = tool_stats_df.loc[(tool_stats_df["Galaxy wrapper id"] == tool_id), "count"] + counts = tool_stats_df.loc[(tool_stats_df["Suite ID"] == tool_id), "count"] agg_versions = counts.sum() # aggregate all counts for all tools in the suite @@ -272,29 +265,28 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, if tool.type != "dir": return None - # the folder of the tool is used as Galaxy wrapper id (maybe rather use the .shed.yml name) - metadata = { - "Galaxy wrapper id": tool.name, - "Galaxy tool ids": [], + metadata: dict = { + "Suite ID": None, + "Tool IDs": [], "Description": None, - "bio.tool id": None, - "bio.tool ids": set(), # keep track of multi IDs - "biii": None, + "Suite first commit date": None, + "Homepage": None, + "Suite version": None, + "Suite conda package": None, + "Latest suite conda package version": None, + "Suite version status": "To update", + "ToolShed categories": [], + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": None, + "Suite source": None, # this is what it written in the .shed.yml + "Suite parsed folder": None, # this is the actual parsed file + "bio.tool ID": None, "bio.tool name": None, "bio.tool description": None, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": None, - "ToolShed categories": [], - "ToolShed id": None, - "Date of first commit of the suite": None, - "Galaxy wrapper owner": None, - "Galaxy wrapper source": None, # this is what it written in the .shed.yml - "Galaxy wrapper parsed folder": None, # this is the actual parsed file - "Galaxy wrapper version": None, - "Conda id": None, - "Conda version": None, + "biii ID": None, } # extract .shed.yml information and check macros.xml try: @@ -310,11 +302,11 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, metadata["Description"] = get_shed_attribute("long_description", yaml_content, None) if metadata["Description"] is not None: metadata["Description"] = metadata["Description"].replace("\n", "") - metadata["ToolShed id"] = get_shed_attribute("name", yaml_content, None) - metadata["Galaxy wrapper owner"] = get_shed_attribute("owner", yaml_content, None) - metadata["Galaxy wrapper source"] = get_shed_attribute("remote_repository_url", yaml_content, None) + metadata["Suite ID"] = get_shed_attribute("name", yaml_content, None) + metadata["Suite owner"] = get_shed_attribute("owner", yaml_content, None) + metadata["Suite source"] = get_shed_attribute("remote_repository_url", yaml_content, None) if "homepage_url" in yaml_content: - metadata["Source"] = yaml_content["homepage_url"] + metadata["Homepage"] = yaml_content["homepage_url"] metadata["ToolShed categories"] = get_shed_attribute("categories", yaml_content, []) if metadata["ToolShed categories"] is None: metadata["ToolShed categories"] = [] @@ -324,10 +316,10 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, assert isinstance(file_list, list) # store the github location where the folder was parsed - metadata["Galaxy wrapper parsed folder"] = tool.html_url + metadata["Suite parsed folder"] = tool.html_url # get the first commit date - metadata["Date of first commit of the suite"] = shared.get_first_commit_for_folder(tool, repo) + metadata["Suite first commit date"] = shared.get_first_commit_for_folder(tool, repo) # find and parse macro file for file in file_list: @@ -337,18 +329,17 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, for child in root: if "name" in child.attrib: if child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@": - metadata["Galaxy wrapper version"] = child.text + metadata["Suite version"] = child.text elif child.attrib["name"] == "requirements": - metadata["Conda id"] = get_conda_package(child) + metadata["Suite conda package"] = get_conda_package(child) # bio.tools biotools = get_xref(child, attrib_type="bio.tools") if biotools is not None: - metadata["bio.tool id"] = biotools - metadata["bio.tool ids"].add(biotools) + metadata["bio.tool ID"] = biotools # biii biii = get_xref(child, attrib_type="biii") if biii is not None: - metadata["biii"] = biii + metadata["biii ID"] = biii # parse XML file and get meta data from there for file in file_list: @@ -360,11 +351,11 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, print(traceback.format_exc()) else: # version - if metadata["Galaxy wrapper version"] is None: + if metadata["Suite version"] is None: if "version" in root.attrib: version = root.attrib["version"] if "VERSION@" not in version: - metadata["Galaxy wrapper version"] = version + metadata["Suite version"] = version else: macros = root.find("macros") if macros is not None: @@ -372,52 +363,51 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, if "name" in child.attrib and ( child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@" ): - metadata["Galaxy wrapper version"] = child.text + metadata["Suite version"] = child.text # bio.tools biotools = get_xref(root, attrib_type="bio.tools") if biotools is not None: - metadata["bio.tool id"] = biotools - metadata["bio.tool ids"].add(biotools) + metadata["bio.tool ID"] = biotools # biii - if metadata["biii"] is None: + if metadata["biii ID"] is None: biii = get_xref(root, attrib_type="biii") if biii is not None: - metadata["biii"] = biii + metadata["biii ID"] = biii # conda package - if metadata["Conda id"] is None: + if metadata["Suite conda package"] is None: reqs = get_conda_package(root) if reqs is not None: - metadata["Conda id"] = reqs + metadata["Suite conda package"] = reqs # tool ids if "id" in root.attrib: - metadata["Galaxy tool ids"].append(root.attrib["id"]) + metadata["Tool IDs"].append(root.attrib["id"]) # get latest conda version and compare to the wrapper version - if metadata["Conda id"] is not None: - r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Conda id"]}') + if metadata["Suite conda package"] is not None: + r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Suite conda package"]}') if r.status_code == requests.codes.ok: conda_info = r.json() if "latest_version" in conda_info: - metadata["Conda version"] = conda_info["latest_version"] - if metadata["Conda version"] == metadata["Galaxy wrapper version"]: - metadata["Status"] = "Up-to-date" + metadata["Latest suite conda package version"] = conda_info["latest_version"] + if metadata["Latest suite conda package version"] == metadata["Suite version"]: + metadata["Suite version status"] = "Up-to-date" # get bio.tool information - if metadata["bio.tool id"] is not None: - r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool id"]}/?format=json') + if metadata["bio.tool ID"] is not None: + r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool ID"]}/?format=json') if r.status_code == requests.codes.ok: biotool_info = r.json() if "function" in biotool_info: for func in biotool_info["function"]: if "operation" in func: for op in func["operation"]: - metadata["EDAM operation"].append(op["term"]) + metadata["EDAM operations"].append(op["term"]) if "topic" in biotool_info: for t in biotool_info["topic"]: - metadata["EDAM topic"].append(t["term"]) + metadata["EDAM topics"].append(t["term"]) if "name" in biotool_info: metadata["bio.tool name"] = biotool_info["name"] if "description" in biotool_info: @@ -549,19 +539,17 @@ def export_tools_to_tsv( :param format_list_col: boolean indicating if list columns should be formatting """ - df = pd.DataFrame(tools).sort_values("Galaxy wrapper id") + df = pd.DataFrame(tools).sort_values("Suite ID") if format_list_col: df["ToolShed categories"] = shared.format_list_column(df["ToolShed categories"]) - df["EDAM operation"] = shared.format_list_column(df["EDAM operation"]) - df["EDAM topic"] = shared.format_list_column(df["EDAM topic"]) + df["EDAM operations"] = shared.format_list_column(df["EDAM operations"]) + df["EDAM topics"] = shared.format_list_column(df["EDAM topics"]) - df["EDAM operation (no superclasses)"] = shared.format_list_column(df["EDAM operation (no superclasses)"]) - df["EDAM topic (no superclasses)"] = shared.format_list_column(df["EDAM topic (no superclasses)"]) - - df["bio.tool ids"] = shared.format_list_column(df["bio.tool ids"]) + df["EDAM reduced operations"] = shared.format_list_column(df["EDAM reduced operations"]) + df["EDAM reduced topics"] = shared.format_list_column(df["EDAM reduced topics"]) # the Galaxy tools need to be formatted for the add_instances_to_table to work - df["Galaxy tool ids"] = shared.format_list_column(df["Galaxy tool ids"]) + df["Tool IDs"] = shared.format_list_column(df["Tool IDs"]) if to_keep_columns is not None: df = df[to_keep_columns] @@ -576,8 +564,7 @@ def add_status(tool: Dict, tool_status: Dict) -> None: :param tool: dictionary with tools and their metadata :param tool_status: dictionary with tools and their 2 status: Keep and Deprecated """ - name = tool["Galaxy wrapper id"] - tool["Reviewed"] = name in tool_status + name = tool["Suite ID"] if name in tool_status: tool["To keep"] = tool_status[name]["To keep"] tool["Deprecated"] = tool_status[name]["Deprecated"] @@ -624,7 +611,7 @@ def curate_tools( add_status(tool, tool_status) if tool["To keep"]: # only add tools that are manually marked as to keep curated_tools.append(tool) - if tool["bio.tool id"] is None: + if tool["bio.tool ID"] is None: tools_wo_biotools.append(tool) else: tools_with_biotools.append(tool) @@ -695,15 +682,12 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: # add additional information to tools for tool in tools: # add EDAM terms without superclass - tool["EDAM operation (no superclasses)"] = reduce_ontology_terms(tool["EDAM operation"], ontology=edam_ontology) - tool["EDAM topic (no superclasses)"] = reduce_ontology_terms(tool["EDAM topic"], ontology=edam_ontology) + tool["EDAM reduced operations"] = reduce_ontology_terms(tool["EDAM operations"], ontology=edam_ontology) + tool["EDAM reduced topics"] = reduce_ontology_terms(tool["EDAM topics"], ontology=edam_ontology) # add availability for UseGalaxy servers for name, url in USEGALAXY_SERVER_URLS.items(): - tool[f"Available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) - # add availability for all UseGalaxy servers - for name, url in USEGALAXY_SERVER_URLS.items(): - tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) + tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) # add all other available servers public_servers_df = pd.read_csv(public_servers, sep="\t") @@ -715,12 +699,12 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: ]: # do not query UseGalaxy servers again url = row["url"] - tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) + tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) # add tool stats for name, path in GALAXY_TOOL_STATS.items(): tool_stats_df = pd.read_csv(path) - tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Galaxy tool ids"]) + tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Tool IDs"]) # sum up tool stats for names_to_match in GALAXY_TOOL_STATS_SUM: @@ -728,7 +712,7 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: for col_name in tool.keys(): if names_to_match in col_name: summed_stat += tool[col_name] - tool[f"{names_to_match} - all main servers"] = summed_stat + tool[f"{names_to_match} on main servers"] = summed_stat return tools @@ -862,7 +846,7 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: filtered_tools, args.tsv_filtered, format_list_col=True, - to_keep_columns=["Galaxy wrapper id", "Description", "To keep", "Deprecated"], + to_keep_columns=["Suite ID", "Description", "To keep", "Deprecated"], ) else: # if there are no ts filtered tools @@ -889,13 +873,13 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: tools_wo_biotools, args.wo_biotools, format_list_col=True, - to_keep_columns=["Galaxy wrapper id", "Source", "Galaxy wrapper source"], + to_keep_columns=["Suite ID", "Homepage", "Suite source"], ) export_tools_to_tsv( tools_with_biotools, args.w_biotools, format_list_col=True, - to_keep_columns=["Galaxy wrapper id", "bio.tool name", "EDAM operation", "EDAM topic"], + to_keep_columns=["Suite ID", "bio.tool name", "EDAM operations", "EDAM topics"], ) else: # if there are no ts filtered tools diff --git a/sources/bin/format_tools.sh b/sources/bin/format_tools.sh index ecf25c2a..6514c887 100755 --- a/sources/bin/format_tools.sh +++ b/sources/bin/format_tools.sh @@ -8,8 +8,8 @@ if [[ ! -z $1 && $1 == "test" ]]; then python sources/bin/create_wordcloud.py \ --input "communities/all/resources/test_tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite users on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/all/resources/tools_wordcloud.png" else @@ -20,8 +20,8 @@ else python sources/bin/create_wordcloud.py \ --input "communities/all/resources/tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite users on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/all/resources/tools_wordcloud.png" fi; \ No newline at end of file diff --git a/sources/bin/get_community_tools.sh b/sources/bin/get_community_tools.sh index 165940b5..4b2772c4 100755 --- a/sources/bin/get_community_tools.sh +++ b/sources/bin/get_community_tools.sh @@ -6,7 +6,7 @@ set -e if [[ ! -z $1 && $1 == "test" ]]; then python sources/bin/extract_galaxy_tools.py \ filter \ - --all "communities/all/resources/tools.json" \ + --all "communities/all/resources/test_tools.json" \ --categories "communities/microgalaxy/metadata/categories" \ --tsv-filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv" \ --filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.json" \ @@ -20,18 +20,10 @@ if [[ ! -z $1 && $1 == "test" ]]; then --wo-biotools "communities/microgalaxy/resources/curated_tools_wo_biotools.tsv" \ --w-biotools "communities/microgalaxy/resources/curated_tools_w_biotools.tsv" - python sources/bin/create_interactive_table.py \ - --input "communities/microgalaxy/resources/curated_tools.tsv" \ - --remove-col "Reviewed" \ - --remove-col "To keep" \ - --filter-col "To keep" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/microgalaxy/resources/tools.html" - python sources/bin/create_wordcloud.py \ --input "communities/microgalaxy/resources/curated_tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite runs (last 5 years) on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/microgalaxy/resources/tools_wordcloud.png" @@ -62,19 +54,11 @@ else --wo-biotools "communities/$community/resources/curated_tools_wo_biotools.tsv" \ --w-biotools "communities/$community/resources/curated_tools_w_biotools.tsv" - if [[ -e "communities/$community/resources/curated_tools.tsv" && -f "communities/$community/resources/curated_tools.tsv" ]]; then - python sources/bin/create_interactive_table.py \ - --input "communities/$community/resources/curated_tools.tsv" \ - --remove-col "Reviewed" \ - --remove-col "To keep" \ - --filter-col "To keep" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/$community/resources/tools.html" - + if [[ -e "communities/$community/resources/curated_tools.tsv" && -f "communities/$community/resources/curated_tools.tsv" ]]; then python sources/bin/create_wordcloud.py \ --input "communities/$community/resources/curated_tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite runs (last 5 years) on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/$community/resources/tools_wordcloud.png" fi;