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ProteomicsLFQ documentation issues #6092

Open hendrikweisser opened 2 years ago

hendrikweisser commented 2 years ago

The ProteomicsLFQ documentation should be improved (especially since it's now being used in nf-core workflows). See current state here: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html

  1. Parameters are missing (i.e. the section below - not sure if UTILS_ProteomicsLFQ is correct) 
    <B>The command line parameters of this tool are:</B>
@verbinclude UTILS_ProteomicsLFQ.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_ProteomicsLFQ.html
  2. What does "picked protein FDR" mean (parameter "picked_proteinFDR")?
  3. "experiments TODO" section probably shouldn't be written out
jpfeuffer commented 2 years ago

Let me know if you need help. I will lookup the picked proteinfdr paper but essentially it just looks at targets and decoys in pairs and removes both of them from the list of candidates once one of them was considered.

jpfeuffer commented 2 years ago

1 was done in #6213