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rickhelmus / patRoon

Workflow solutions for mass-spectrometry based non-target analysis.
https://rickhelmus.github.io/patRoon/
GNU General Public License v3.0
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Feature Suggestion: Import SIRIUS results (formula & compound) #57

Open drewszabo opened 1 year ago

drewszabo commented 1 year ago

Hey Rick,

With all the recent changes to SIRIUS in v5 (and the deprecation of v4), I think it would be useful to allow patRoon to import SIRIUS output generated by users who prefer the standalone-CLI or the GUI. I suppose it would be similar to the XCMS import that patRoon offers in feature finding. Furthermore, it seems (at least with recent versions of SIRIUS) that formulas are generated concurrently with compound generation. It would significantly reduce compute time if patRoon could fetch both formula and compound results from the generateCompoundsSIRIUS() function. Or in addition to my first point, allow patRoon to import formulas from SIRIUS CLI/GUI results.

I can see you are already integrating SIRIUS v5 into patRoon, so perhaps you have already considered this! If so, please disregard 👍

rickhelmus commented 1 year ago

Hi @drewszabo,

Thanks for your feedback! I think these are pretty good ideas. Doing the formulas and compounds could indeed be a nice time saver :-) I would need to investigate a bit, but I think it's fairly straightforward to import data from multiple workflow steps.

Thanks, Rick