Use of Pangolin after MultiQC v1.11

galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

https://galaxyproject.org/iuc

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Use of Pangolin after MultiQC v1.11 #4444

Open BenjaminDEMAILLE opened 2 years ago

BenjaminDEMAILLE commented 2 years ago

Good Morning We trie to use your version of MultiQC on Galaxy with pangolin. We seen that MultQC v 1.11 support pangolin. But when we want to use it on Galaxy, we seem to have a problem for pangolin not being supported by the multiqc tool in Galaxy. When we check the wrapper (https://github.com/galaxyproject/tools-iuc/blob/master/tools/multiqc/multiqc.xml) we don’t see any mention of Pangolin. How can we add it ?

Thanks a lot in advance ! Best regards Benjamin Demaille

bernt-matthias commented 2 years ago

Dear @BenjaminDEMAILLE

One would need to:

add pangoling to the tool select: https://github.com/galaxyproject/tools-iuc/blob/5fcc308928ab2417b7e40227b27a3955f227649d/tools/multiqc/multiqc.xml#L225
add a corresponding when block below this that contains the data input parameter
extend the command line by adding pangolin to the huge if-else block starting here https://github.com/galaxyproject/tools-iuc/blob/5fcc308928ab2417b7e40227b27a3955f227649d/tools/multiqc/multiqc.xml#L24
add a test

Need any help with this / further explanation? Could you contribute this?

bgruening commented 2 years ago

@BenjaminDEMAILLE if you can make a start that would be awesome.

There will be soon new modules in MQC that we also would like to include: gfastats, genomescope2, merqury, pretext and hifiasm. So we can help with that of course.

BenjaminDEMAILLE commented 2 years ago

Dear @bgruening / @bernt-matthias unfortunately, I'm not very conformable with the xml format. I'm newbie in galaxy development