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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Friday, June 30 • 15:20 - 16:35
P10: ToolDog - generating tool descriptors from the ELIXIR tool registry

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Kenzo-Hugo Hillion 1*, Ivan Kuzmin 2, Hedi Peterson 2, Jon Ison 3, Hervé Ménager 1*

1 : Center of Bioinformatics, Biostatistics and Integrative Biology  (C3BI)Institut Pasteur de Paris
2 : Institute of Computer Science, University of Tartu
3 : Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark* : Corresponding author

Over the last years, the use of bioinformatics tools has been eased by the use of workbench systems such as Galaxy or frameworks that use the Common Workflow Language (CWL). Still, the integration of these resources in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete description of tools that are often missing information such as some parameters, a description or metadata.

ToolDog (Tool DescriptiOn Generator) is the main component of the Workbench Integration Enabler service of the ELIXIR bio.tools registry. The goal of this tool is to guide the integration of tools into workbench environments. In order to do that, ToolDog is divided in two main parts: the first part analyses the source code of the bioinformatics software with language dedicated tools and generates a Galaxy XML or CWL tool description. Then, the second part is dedicated to the annotation of the generated tool description using metadata provided by bio.tools. This annotator can also be used on its own to enrich existing tool descriptions with missing metadata such as the recently developed EDAM annotation.


Kenzo-Hugo Hillion

Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI); Institut Pasteur de Paris

Friday June 30, 2017 15:20 - 16:35
Le Corum Le Corum

Attendees (6)