Using bio.tools to generate and annotate workbench tool descriptions

Kenzo-Hugo Hillion; Ivan Kuzmin; Anton Khodak; Eric Rasche; Michael Crusoe; Hedi Peterson; Jon Ison; Hervé Ménager

doi:10.12688/f1000research.12974.1

Using bio.tools to generate and annotate workbench tool descriptions

Kenzo-Hugo Hillion^*, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager

^*Corresponding author for this work

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Abstract

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 A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation.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.

Original language	English
Article number	2074
Journal	F1000Research
Volume	6
Number of pages	14
ISSN	2046-1402
DOIs	https://doi.org/10.12688/f1000research.12974.1
Publication status	Published - 2017

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© 2017 Hillion KH et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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7badfa4e 5cfe 436c 9f0b 99a70bc52910 12974 Herve MenagerFinal published version, 2.38 MB

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title = "Using bio.tools to generate and annotate workbench tool descriptions",

abstract = "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.",

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AU - Hillion, Kenzo-Hugo

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AU - Rasche, Eric

AU - Crusoe, Michael

AU - Peterson, Hedi

AU - Ison, Jon

AU - Ménager, Hervé

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N2 - 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.

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Using bio.tools to generate and annotate workbench tool descriptions

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