[24.1] xsd: allow change_format and actions also in statically defined collection elements, and break recursion

[bernt-matthias]

also those contained in collections. Used for instance here:

https://github.com/galaxyproject/tools-iuc/blob/695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82/tools/hybpiper/hybpiper.xml#L198 https://github.com/galaxyproject/tools-iuc/blob/695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82/tools/krakentools/extract_kraken_reads.xml#L145

The recursive static definition of nested collections is not clear to me. Could not find any example.

Could also target 24.1

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[mvdbeek]

If these work then we should add this as a bug fix to 24.1

[bernt-matthias]

In the commit message of #17236 you noted that change_format is not implemented: https://github.com/galaxyproject/tools-iuc/blob/695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82/tools/krakentools/extract_kraken_reads.xml#L145

I'm not sure about this, the parser uses the same function for data in collection elements as for top level data elements.

I think the recursion in the xsd has been introduced also i this PR, or?

[bernt-matthias]

Should be about it.

• I think discover_datasets in collection - data makes no sense. I will remove it.
  • also seems not possible, gave me Cannot pre-determine structure for collection of type list when I tried it.
• Would like to test if filter in collection - data works. Would be fancy, but I can not think of a use case.
  • Does not work (see c0ce2a7): For paired collection the definition is impossible, since we can not have multiple collection elements with the same name. For list the filter just does not work.
• Add a test for action in collection - data

[mvdbeek]

That looks like a solid cleanup, thank you!