Add Galaxy wrapper for motus map_snv

[xens25]

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)

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.

[xens25]

Hi @SaimMomin12 . This is the map_snv tool for motus.

[SaimMomin12]

Some comments inline

[SaimMomin12]

@xens25 @VERSION_SUFFIX@ and @PROFILE@ needs to be added to macros.xml

[xens25]

@SaimMomin12 After updating the macros, the tests are failing but they pass in the terminal. Did I add something incorrectly?

[SaimMomin12]

@SaimMomin12 After updating the macros, the tests are failing but they pass in the terminal. Did I add something incorrectly?

@xens25 See here: https://github.com/bgruening/galaxytools/actions/runs/22862161392/job/66366094632?pr=1796

.. WARNING: remote_repository_url may be incorrect: expected it to end with a significant part of '/home/runner/work/galaxytools/galaxytools/tools/motus'

[xens25]

@SaimMomin12 After updating the macros, the tests are failing but they pass in the terminal. Did I add something incorrectly?

@xens25 See here: https://github.com/bgruening/galaxytools/actions/runs/22862161392/job/66366094632?pr=1796

.. WARNING: remote_repository_url may be incorrect: expected it to end with a significant part of '/home/runner/work/galaxytools/galaxytools/tools/motus'

Thanks. After this last update, the test passed. The remaining lint error comes from the motus_profiler.xml which also fails in my terminal. Should I fix that file?

[SaimMomin12]

@SaimMomin12 After updating the macros, the tests are failing but they pass in the terminal. Did I add something incorrectly?

@xens25 See here: https://github.com/bgruening/galaxytools/actions/runs/22862161392/job/66366094632?pr=1796

.. WARNING: remote_repository_url may be incorrect: expected it to end with a significant part of '/home/runner/work/galaxytools/galaxytools/tools/motus'

Thanks. After this last update, the test passed. The remaining lint error comes from the motus_profiler.xml which also fails in my terminal. Should I fix that file?

The remaining linter error is due to unavailability of mgc and bam_no_index datatypes, although they aren't part of the Galaxy Datatypes. We can leave it for now.

[SaimMomin12]

@bgruening The deployment failed, could you please assist here?

[bgruening]

I see this here:

+Linting tool /home/runner/work/galaxytools/galaxytools/tools/motus/motus_profiler.xml
.. ERROR (ValidDatatypes): Unknown datatype [mgc] used in param element
.. ERROR (ValidDatatypes): Unknown datatype [bam_no_index] used in data element

[SaimMomin12]

I see this here:

+Linting tool /home/runner/work/galaxytools/galaxytools/tools/motus/motus_profiler.xml

.. ERROR (ValidDatatypes): Unknown datatype [mgc] used in param element

.. ERROR (ValidDatatypes): Unknown datatype [bam_no_index] used in data element

Those datatypes do not exist imo