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"fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "jison", "additionDate": "2018-12-12T12:35:31Z", "lastUpdate": "2026-03-25T12:24:23.606945Z", "editPermission": { "type": "group", "authors": [ "hans" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ToolDog", "description": "This tool aims to generate XML template for Galaxy or CWL from the description of tools from the bio.tools registry.", "homepage": "https://github.com/bio-tools/ToolDog", "biotoolsID": "tooldog", "biotoolsCURIE": "biotools:tooldog", "version": [ "0.3.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bio-tools/ToolDog", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bio-tools/ToolDog/archive/v0.3.5.tar.gz", "type": "Source code", "note": "Download link to v.0.3.5", "version": null } ], "documentation": [ { "url": "http://tooldog.readthedocs.io/en/latest/?badge=latest", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.12974.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Using bio.tools to generate and annotate workbench tool descriptions", "abstract": "© 2017 Hillion KH et al.Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.", "date": "2017-01-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Hillion K.-H." }, { "name": "Kuzmin I." }, { "name": "Khodak A." }, { "name": "Rasche E." }, { "name": "Crusoe M." }, { "name": "Peterson H." }, { "name": "Ison J." }, { "name": "Menager H." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": "https://research.pasteur.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics Hub", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "Hervé Ménager", "email": "hmenager@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Kenzo-Hugo Hillion", "email": "kehillio@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "khillion", "additionDate": "2017-12-21T07:28:12Z", "lastUpdate": "2018-12-10T12:58:59Z", "editPermission": { "type": "group", "authors": [ "hmenager" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }