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WGS-TB / MentaLiST

The MLST pipeline developed by the PathOGiST research group
MIT License
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Galaxy cgMLST data manager appears to be missing some options #79

Open apetkau opened 5 years ago

apetkau commented 5 years ago

If I take a look at the current Galaxy cgMLST options, I can see an option for Mycobacterium tuberculosis/bovis/africanum/canettii and Klebsiella pneumoniae/variicola/quasipneumoniae (https://github.com/WGS-TB/MentaLiST/blob/master/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml#L23).

But, if I look at the same file in the Galaxy tool version (https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=abb1bdef1d34c798) those options appear to be missing.

dfornika commented 5 years ago

Thanks, I think this should be a simple fix if we just add those entries to the xml file. It would be nice to have a way to automatically sync that list with what is available on cgMLST.org, but I don't have a solution for that in mind right now.

apetkau commented 5 years ago

Awesome. Thanks.

Yeah, it would be nice if it was automated. I'm not sure if any other Galaxy tool is able to automatically sync options from some remote server. I'll keep an eye out for one though. Maybe there's a way to get it working.

dfornika commented 5 years ago

Related: https://github.com/WGS-TB/MentaLiST/issues/35