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

Research output: Contribution to journalJournal articleResearchpeer-review

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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 A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation.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 languageEnglish
Article number2074
JournalF1000Research
Volume6
Number of pages14
ISSN2046-1402
DOIs
Publication statusPublished - 2017

Bibliographical note

© 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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