Add tsebra #5483
Add tsebra #5483
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You test files are too big. Howver you could just remove them as you do not need them currently. You only test with asserts.
However, I think we should use them, at least a part of it. It wil be good with future updates to see (in a future diff) what has changed and if the GTFs still look good.
You could remove most of the lines of your test-files and then use contains
file="mode_mp_output1.gff" ftype="gff" compare="contains"/>
https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output
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The rest looks really great @rlibouba! |
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I'm having difficulty with the second test, in particular with the second output generated by the --score_tab parameter. In one column, the rounding of the numbers is not always the same, which causes the test to fail. When I run the tests locally with planemo test, the tests pass |
tools/tsebra/tsebra.xml
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| <param name="gtf_file" argument="-g" type="data" format="gtf" optional="true" label="List of gene prediciton files"/> | ||
| <param name="keep_gtf" argument="-k" type="data" format="gtf" optional="true" label="Gene prediction list" help="All transcripts from these gene sets will be included in the output"/> | ||
| <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/> | ||
| <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/> |
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All 4 inputs are optional, in theory a user can start this tool without inputs, I think this should not happen.
Do you have a smart idea here @rlibouba ?
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Hi Björn, thank you for your return. I've suggested something for that. What do you think?
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Do you need help with the failing test? |
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Yes, I'd like to. Thank you. I don't understand the error output in relation to the choice of tests. The numbers in the penultimate column are completely different. |
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Looks like the test file is not up to date. You could use asserts and not file comparisons if this helps. |
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Thanks @rlibouba |
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Attention: deployment skipped! https://github.com/galaxyproject/tools-iuc/actions/runs/6577288426 |
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@rlibouba running it on master resulted in: Is this output a bit random? Do you need to sort it? |
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I've created a PR for the update. All tests passed. There were no major changes to the files. |
FOR CONTRIBUTOR: