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required parameter

advanced parameter

+PeptideIndexerRefreshes the protein references for all peptide hits.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'PeptideIndexer'

in Input idXML file containing the identifications.input file*.idXML

fasta Input sequence database in FASTA format. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'input file*.fasta

out Output idXML file.output file*.idXML

decoy_string_rev String that was appended (or prepended - see 'prefix' flag below) to the accession of the protein database to indicate a decoy protein.

missing_decoy_actionerror Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)error,warn

write_protein_sequencefalse If set, the protein sequences are stored as well.true,false

prefixfalse If set, the database has protein accessions with 'decoy_string' as prefix.true,false

keep_unreferenced_proteinsfalse If set, protein hits which are not referenced by any peptide are kept.true,false

allow_unmatchedfalse If set, unmatched peptide sequences are allowed. By default (i.e. this flag is not set) the program terminates with error status on unmatched peptides.true,false

full_tolerant_searchfalse If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous AA's) are associated. This is much slower!true,false

aaa_max4 Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'0:∞

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false