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Use new group_tag parameter to allow selecting collection subsets #2167

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merged 2 commits into from Feb 4, 2019

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mvdbeek commented Nov 6, 2018

The idea here is that the user tags elements of a collection using tags that
start with group:. All of these tags can then be selected in the tool
form when choosing the factor levels.
This makes it very easy to select dataset combinations of interest
without having to re-shape collection contents for every contrast.

Technically the input does not need to be a collection, a
multiple="true" data input also works, but is currently not testable.
We might change this in the future.

The previous way of doing the analysis is still the default way of
using deseq2, as we currently don't auto-propagate group tags.
So in order to use this new feature users either have to manually tag collection
elements or use the Tag elements from file from contents of a file
to set the group tags. Hopefully we will enable auto-propagation
in 19.01 and enhance the apply rules tool to manipulate group tags.

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

FOR REVIEWER:

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mvdbeek commented Nov 7, 2018

I guess we need to update the xsd schema for the tags attribute ...

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mvdbeek commented Nov 19, 2018

Yay, all green with the new planemo release!

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bgruening left a comment

That's super cool and LGTM.
Merci @mvdbeek

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davebx approved these changes Jan 14, 2019

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davebx commented Jan 14, 2019

I agree with Björn.

@mvdbeek mvdbeek force-pushed the mvdbeek:deseq2_group_tags branch from bd23efc to d79f333 Feb 3, 2019

mvdbeek added some commits Nov 6, 2018

Use new group_tag parameter to allow selecting collection subsets
The idea here is that the user tags elements of a collection using tags that
start with `group:`. All of these tags can then be selected in the tool
form when choosing the factor levels.
This makes it very easy to select dataset combinations of interest
without having to re-shape collection contents for every contrast.

Technically the input does not need to be a collection, a
multiple="true" data input also works, but is currently not testable.
We might change this in the future.

The previous way of doing the analysis is still the default way of
using deseq2, as we currently don't auto-propagate group tags.
So in order to use this new feature users either have to manually tag collection
elements or use the `Tag elements from file from contents of a file`
to set the group tags. Hopefully we will enable auto-propagation
in 19.01 and enhance the apply rules tool to manipulate group tags.

@mvdbeek mvdbeek force-pushed the mvdbeek:deseq2_group_tags branch from d79f333 to 6a62f6c Feb 3, 2019

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mvdbeek commented Feb 4, 2019

Corresponding mini-tutorial here: galaxyproject/training-material#1244

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bgruening commented Feb 4, 2019

Merci @mvdbeek!

@bgruening bgruening merged commit 1b60ee0 into galaxyproject:master Feb 4, 2019

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