Alter tsv outcome

[marissaDubbelaar]

Description of feature

Make sure that the outcome TSV is changed to a more readable format since this content is not ready to be used for analysis immediately.
A suggestion is that the current TSV be stored under intermediate results.

[jonasscheid]

We could use csvtk or csvkit suite to truncate the output. We definitely need to handle the quant TSV files differently before that

[jonasscheid]

I think a custom python script is best, since we have the possibility to generate columns that multiQC can visualize easily downstream

[marissaDubbelaar]

If it can be handled like that, that would be great. Especially if it might aid in the multiqc figures

[jonasscheid]

We should use pyopenms to directly read the idXML filtered output. Potentially also the consensusXML output of quant-mode

[marissaDubbelaar]

Yea that sounds good to me 👍

[jonasscheid]

Additional note here: mzTab files for ID-mode (not --quantify) can be removed since they are only used for PRIDE uploads, but PRIDE requests quantification values in mzTab format.