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galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
MIT License
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DecoyDatabase bug #708

Closed neoformit closed 1 year ago

neoformit commented 1 year ago

We received a ticket on usegalaxy.org.au reporting that the -method reverse param of DecoyDatabase does not work (that is, sequences are shuffled for both reverse and shuffled options).

Looking at the wrapper it seems like the error must lie in the fill_ctd.py script that appears to write an ini file.

neoformit commented 1 year ago

Also the test-data for DecoyDatabase is missing so I can't run the tests

bernt-matthias commented 1 year ago

Test data for OpenMS is huge. So its at the moment generated with test-data.sh.

bernt-matthias commented 1 year ago

You could check if fill_ctd.py creates the correct entries in the ini file.

bernt-matthias commented 1 year ago

Seems that the Galaxy tool is correct, but the OpenMS docs quite confusing: https://github.com/OpenMS/OpenMS/pull/6844 .. reverse and shuffle do not act on the whole sequence, but only on each peptide separately .. if I get it right .

Closing this. Feel free to reopen :)

neoformit commented 1 year ago

Thanks @bernt-matthias, will check this out and reply to our confused user.