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Add EDAM operations to tools and expose in API #2379

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merged 3 commits into from May 23, 2016

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@mvdbeek
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commented May 19, 2016

This our (@nsoranzo, @odoppelt) contribution from the TWW Hackathon.

@dannon @jmchilton any comments?

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commented May 19, 2016

Awesome!

@nsoranzo nsoranzo changed the title [WIP] Add edam operations to tools and expose in API [WIP] Add EDAM operations to tools and expose in API May 19, 2016

mvdbeek and others added some commits May 19, 2016

Annotate tools with edam_operations
to demonstrate usage of edam_operations in tool xml.

@nsoranzo nsoranzo force-pushed the mvdbeek:edam_operations branch from 7ac8ce6 to 4221957 May 19, 2016

@mvdbeek mvdbeek changed the title [WIP] Add EDAM operations to tools and expose in API Add EDAM operations to tools and expose in API May 19, 2016

@mvdbeek mvdbeek added status/review and removed status/WIP labels May 19, 2016

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commented May 19, 2016

Ready for review.

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commented May 19, 2016

👍 Looks perfect to me - what percentage of tools should have an EDAM operation?

  • All tools
  • Most bioinformatics tools
  • Some bioinformatics tools
  • Some tools

If it is all tools we should add a planemo lint for this also. If it is just most or all bioinformatics tools - maybe we should add a planemo linter for that keyed on like a --bioinformatics flag for instance. If useful there are other things we can do with --bioinformatics such as check that the datatypes are in Galaxy core.

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commented May 19, 2016

EDAM provides ontologies for bioinformatics, so I'd say "most bioinformatics tools". Regarding planemo lint, it could at least verify that it is structured correctly if it is present.

@jmchilton jmchilton merged commit 7c3622d into galaxyproject:dev May 23, 2016

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commented May 23, 2016

@mvdbeek @nsoranzo @odoppelt @jmchilton quick question: could/should we add a way to also specify EDAM topics in this? Something like an <edam_topic> element?

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commented May 23, 2016

@hmenager Sure, EDAM topic is also a mandatory attribute for bio.tools registration: https://github.com/bio-tools/biotoolsxsd

@mvdbeek mvdbeek deleted the mvdbeek:edam_operations branch Nov 23, 2016

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