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F1000Res. 2017 Nov 30;6. pii: ELIXIR-2074. doi: 10.12688/f1000research.12974.1. eCollection 2017.

Using bio.tools to generate and annotate workbench tool descriptions.

Author information

1
Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris, France.
2
Institute of Computer Science, University of Tartu, Tartu, Estonia.
3
Igor Sikorsky Kyiv Polytechnic Institute, National Technical University of Ukraine, Kyiv, Ukraine.
4
Lehrstuhl für Bioinformatik, Institut für Informatik, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
5
Common Workflow Language Project, Vilnius, Lithuania.
6
DTU Bioinformatics, Technical University of Denmark, Copenhagen, Denmark.

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 A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation.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

KEYWORDS:

bioinformatics; common workflow language; galaxy; interoperability; registry; tool integration

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