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computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching
GNU General Public License v3.0
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mspurity remarks #22

Closed bernt-matthias closed 4 years ago

bernt-matthias commented 5 years ago

I would remove the input from filesystem:

https://github.com/computational-metabolomics/mspurity-galaxy/blob/f4b9813e5ac0ac76ce8dda955408a72a5d6c7de6/tools/msPurity/purityA.xml#L68

You may also consider to make this https://github.com/computational-metabolomics/mspurity-galaxy/blob/f4b9813e5ac0ac76ce8dda955408a72a5d6c7de6/tools/msPurity/purityA.xml#L64

a type="data" input field with multiple="true". Then users can upload collections and selections of 1 or more data sets.

Tomnl commented 5 years ago

Good points

The library option is available for historic workflows but I could remove for future versions of the tool.

I will look into changing the input type as well

bernt-matthias commented 5 years ago

Another one: does createDatabase really need the libgfortran requirement?

Tomnl commented 5 years ago

This was a temp fix so that I could get CAMERA to install (I think..) as I was getting some errors. (createDatabase - can use the CAMERA object instead of an XCMS object if required).

I will check to see if it is still a problem and the extra requirement can be removed

Tomnl commented 4 years ago

Both issues now addressed