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+IDPosteriorErrorProbabilityEstimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.

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

++1Instance '1' section for 'IDPosteriorErrorProbability'

in input file input file*.idXML

out output file output file*.idXML

output_name gnuplot file as txtoutput file*.txt

smallest_e_value1e-19 This value gives a lower bound to E-Values. It should not be 0, as transformation in a real number (log of E-value) is not possible for certain values then.

split_chargefalse The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed.true,false

top_hits_onlyfalse If set only the top hits of every PeptideIdentification will be usedtrue,false

fdr_for_targets_smaller0.05 Only used, when top_hits_only set. Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run.

ignore_bad_datafalse If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through.true,false

prob_correctfalse If set scores will be calculated as 1-ErrorProbabilities and can be interpreted as probabilities for correct identifications.true,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

+++fit_algorithmAlgorithm parameter subsection

number_of_bins100 Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized

output_plotsfalse If true every step of the EM-algorithm will be written to a file as a gnuplot formulatrue,false

output_name If output_plots is on, the output files will be saved in the following manner: scores.txt for the scores and which contains each step of the EM-algorithm e.g. output_name = /usr/home/OMSSA123 then /usr/home/OMSSA123_scores.txt, /usr/home/OMSSA123 will be written. If no directory is specified, e.g. instead of '/usr/home/OMSSA123' just OMSSA123, the files will be written into the working directory.output file

incorrectly_assignedGumbel for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used.Gumbel,Gauss