Possibility to directly integrate/reuse DecoID in (R-based) annotation workflows?

[jorainer]

Dear developers. We are developing a couple of R packages for analysis of MS data over at RforMassSpectrometry, including also xcms which can be combined in a very flexible way to create reproducible LC-MS(/MS) analysis workflows. I think it would be great if there was the possibility to easily integrate/embed also your DecoID in such workflows. While we could export experimental MS/MS spectra to csv (or msp) files and use them as input to your tool, it would be maybe more efficient to directly provide such data as a python data structure instead. Is there a possibility to call directly the python functions providing the data as a python object/representation? Maybe this already possible and I've just overlooked it - in that case, could you point me to the API/relevant documentation for that?

All this would simplify usage and improve user experience, which I believe would be important to ensure reliable and reproducible analyses.

Thanks in advance for any feedback!

Maybe as additional info: we did already successfully integrate python packages (matchms) into R through the SpectriPy package, that internally converts our MS data structures in R to python data structures, calls the python functions from the library and returns and converts its results back into R.