dissociation method and Luciphor

[ypriverol]

Description of the bug

When using dissociation method, annotation of the CV term with the full term (e.g. COLLISION-INDUCED DISSOCIATION). Luciphor do not understand that parameter because it only understands CID or HCD. We must need to translate some of those terms into CID and HCD, or if the fragmentation method is selected, then use that parameter.

LuciphorAdapter \
      -id kidney_26_3_consensus_fdr_filter_pep.idXML \
      -in kidney_26_3.mzML \
      -executable $(find /usr/local/share/luciphor2-*/luciphor2.jar -maxdepth 0) \
      -out kidney_26_3_consensus_fdr_filter_pep_luciphor.idXML \
      -threads 6 \
      -num_threads 6 \
      -target_modifications 'Phospho (S)' 'Phospho (T)' 'Phospho (Y)' \
      -fragment_method COLLISION-INDUCED DISSOCIATION \
       \
       \
       \
      -max_charge_state 4 \
      -max_peptide_length 40 \
      -debug 0 \
      |& tee kidney_26_3_consensus_fdr_filter_pep_luciphor.log

Command used and terminal output

No response

Relevant files

No response

System information

No response