Use new group_tag parameter to allow selecting collection subsets #2167
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
I guess we need to update the xsd schema for the tags attribute ... |
|
Yay, all green with the new planemo release! |
bgruening
approved these changes
Nov 20, 2018
davebx
approved these changes
Jan 14, 2019
|
I agree with Björn. |
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.
|
Corresponding mini-tutorial here: galaxyproject/training-material#1244 |
|
Merci @mvdbeek! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
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 toolform 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 fileto 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:
FOR REVIEWER:
iuchas access to associated toolshed repo(s)<command/>'single quoted'<![CDATA[ ... ]]>tagstextor havingoptional="true"attribute are checked withif str($param)before being usedformatattribute containing datatypes recognised by Galaxy<![CDATA[ ... ]]>tagsThe text was updated successfully, but these errors were encountered: