Taxonomic Update for obitools4 #7921
Open
kpayet26 wants to merge 27 commits into
Open
Conversation
Contributor
Author
|
I think I need that skip-version-check-label, and I'm not able to add it myself. Can someone help me with it? |
change the test in obirefidx and obitag
bernt-matthias
added
the
skip-version-check
Co-authored-by: M Bernt <m.bernt@ufz.de>
Add validator for name_query parameter from obitaxonomy and for integer parameter from obipcr
Add taxonomic options to obigrep, obiannotate and obiuniq
add test for newick output, add conditional for newick output because of incompatible option
add filter by rank option to obitaxonomy, obigrep and obiannotate
| </param> | ||
| <when value="no_taxo"></when> | ||
| <when value="use_taxo"> | ||
| <param name="rank" type="select" label="Restrict to the given taxonomic rank" multiple="true" optional="true"> |
Contributor
There was a problem hiding this comment.
You can also reuse the taxo_macro here. You could add this additional parameter here by using <yield/> (maybe named): see https://planemo.readthedocs.io/en/latest/writing_advanced.html#parameterizing-xml-macros-with-yield
Contributor
Author
There was a problem hiding this comment.
Tried something using <yield/>. Now there is only one single taxo_macro. Please let me know if it's okay.
Co-authored-by: M Bernt <m.bernt@ufz.de>
…t26/tools-iuc into obitools4_taxonomic_update
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Hello,
This PR add a few more tools for taxonomic attribution, manage taxonomic database and more.
Tools added : obitaxonomy, obipcr, obitag, obirefidx and obicomplement.
Additional options for the handling of taxonomic databases will be integrated into all prior tool versions.
FOR CONTRIBUTOR:
There are two labels that allow to ignore specific (false positive) tool linter errors:
skip-version-check: Use it if only a subset of the tools has been updated in a suite.skip-url-check: Use it if github CI sees 403 errors, but the URLs work.