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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Add RBPBench tool wrapper #1360

Closed michauhl closed 7 months ago

michauhl commented 7 months ago

Hi, this is a Galaxy wrapper for the tool RBPBench ( https://github.com/michauhl/RBPBench ). Goal is to bring it to usegalaxy.org. Best, Michael

michauhl commented 7 months ago

Weird, in my local test environment all 8 tests (planemo test .) pass. My environment:

conda create -n rbpbench-planemo -c conda-forge -c bioconda python=3.9
conda activate rbpbench-planemo
pip3 install planemo
pavanvidem commented 7 months ago

is it possible to move the batch_table_wrapper.py to the original tool instead of keeping it in the Galaxy wrapper? It will be easier to maintain on the tool side than on the Galaxy side.

pavanvidem commented 7 months ago

Tests are passing. Maybe @michauhl will move the python script into the tool. Then we are ready to go.

pavanvidem commented 7 months ago

@michauhl will rbp_ids.catrapid.omics.v2.1.human.6plus.txt stay as it is forever or will it change for some reason in the future? Like more proteins? If it is changing based on the tool updates, then it should also go into the tool. It is probably not optimal to maintain that file as tool-data.

michauhl commented 7 months ago

@michauhl will rbp_ids.catrapid.omics.v2.1.human.6plus.txt stay as it is forever or will it change for some reason in the future? Like more proteins? If it is changing based on the tool updates, then it should also go into the tool. It is probably not optimal to maintain that file as tool-data.

I don't plan on changing it. If so I would rather add a new file, with new identifier. The user can supply a custom database of motifs anyway, or single motifs. So no problem.

michauhl commented 7 months ago

@pavanvidem @bgruening Great, thank you for your help!