[24.2] Add bwa_mem2_index directory datatype, framework enhancements for testing directories #19694
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mvdbeek
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| @@ -304,6 +304,7 @@ | |||
| <converter file="archive_to_directory.xml" target_datatype="directory"/> | |||
| </datatype> | |||
| <datatype extension="directory" type="galaxy.datatypes.data:Directory"/> | |||
| <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory"/> | |||
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Wondering if we should subclass and have some basic sanity checks on the contents. At the moment users can upload anything, or?
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subclass yes, checks no. you can already upload anything, I don't want to touch that.
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Why 24.2 😅 - I mean I think switching the upload API for the tool tests is a long standing issue that I'm so excited to see resolved but it is a big thing that should probably be against dev right? |
for tool tests, which were still using upload1.
This was super-confusing when I used an admin key with `galaxy-tool-test`.
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bgruening
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Feb 25, 2025
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="reference" value="bwa_mem2_index" class="Directory"></param> |
| @@ -0,0 +1,17 @@ | |||
| <tool id="use_directory_index" name="Uses directory index" version="1.0" profile="24.2"> | |||
| <command><
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This is essentially a one-liner with a lot of testing work 😅.
The basic need is for a directory datatype, subclasses like
bwa_mem2_indexcan represent most if not all reference data.Here I've switched our primary tool testing function over to target
__FETCH_DATA__(workflow tests are already using this), and I fixed up cwl-style directory uploads which (at least currently) are not working.It is now possible to upload directories in xml tool tests and workflow tests (via planemo and our internal framework).
Also adds
formatinto the expression input object, so we can use format to decide if a workflow step needs to run.How to test the changes?
(Select all options that apply)
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