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required parameter

advanced parameter

+FalseDiscoveryRateEstimates the false discovery rate on peptide and protein level using decoy searches.

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

++1Instance '1' section for 'FalseDiscoveryRate'

in Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input.input file*.idXML

fwd_in Identification input to estimate FDR, forward run.input file*.idXML

rev_in Identification input to estimate FDR, decoy run.input file*.idXML

out Identification output with annotated FDRoutput file*.idXML

proteins_onlyfalse If set, the FDR of the proteins only is calculatedtrue,false

peptides_onlyfalse If set, the FDR of the peptides only is calculatedtrue,false

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

+++algorithmParameter section for the FDR calculation algorithm

q_valuetrue If 'true', the q-values will be calculated instead of the FDRstrue,false

use_all_hitsfalse If 'true' not only the first hit, but all are used (peptides only)true,false

split_charge_variantsfalse If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only).true,false

treat_runs_separatelyfalse If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only).true,false

decoy_string_rev String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only).

add_decoy_peptidesfalse If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score.true,false