Generates an mzTab file from various sources of a pipeline (mainly a ConsensusXML) which can be used for QC plots (e.g. via the R package 'PTX-QC').

pot. predecessor tools	$\longrightarrow$ QualityControl $\longrightarrow$	pot. successor tools
FeatureLinkerUnlabeledKD (or FLs; for consensusXML)		PTX-QC
IDMapper (for featureXMLs)
InternalCalibration

See Quality Control for details.

The command line parameters of this tool are:

QualityControl -- Computes various QC metrics from many possible input files (only the consensusXML is requir
ed). The more optional files you provide, the more metrics you get.
Full documentation: http://www.openms.de/documentation/TOPP_QualityControl.html
Version: 2.5.0-nightly-2020-03-06 Mar  7 2020, 01:22:16, Revision: 84b1398
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  QualityControl <options>

Options (mandatory options marked with '*'):
  -in_cm <file>*                         ConsensusXML input, generated by FeatureLinker. (valid formats: 'con
                                         sensusXML')
  -in_raw <files>                        MzML input (after InternalCalibration, if available) (valid formats:
                                         'mzML')
  -in_postFDR <files>                    FeatureXMLs after FDR filtering (valid formats: 'featureXML')
  -out <file>*                           Output mzTab with QC information (valid formats: 'mzTab')
  -out_cm <file>                         ConsensusXML with QC information (as metavalues) (valid formats: 
                                         'consensusXML')
  -out_feat <files>                      FeatureXMLs with QC information (as metavalues) (valid formats: 'fea
                                         tureXML')

Fragment Mass Error settings:
  -FragmentMassError:unit <unit>         Unit for mass tolerance. 'auto' uses information from FeatureXML 
                                         (default: 'auto' valid: 'auto', 'ppm', 'da')
  -FragmentMassError:tolerance <double>  M/z search window for matching peaks in two spectra (default: '20.0'
                                         )

  -in_contaminants <file>                Proteins considered contaminants (valid formats: 'fasta')
  -in_trafo <file>                       TrafoXMLs from MapAligners (valid formats: 'trafoXML')

MS2 ID Rate settings:
  -MS2_id_rate:force_no_fdr              Forces the metric to run if FDR is missing (accepts all pep_ids as 
                                         target hits).

                                         
Common TOPP options:
  -ini <file>                            Use the given TOPP INI file
  -threads <n>                           Sets the number of threads allowed to be used by the TOPP tool (defa
                                         ult: '1')
  -write_ini <file>                      Writes the default configuration file
  --help                                 Shows options
  --helphelp                             Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+QualityControlComputes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.

version2.5.0-nightly-2020-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QualityControl'

in_cm ConsensusXML input, generated by FeatureLinker.input file*.consensusXML

in_raw[] MzML input (after InternalCalibration, if available)input file*.mzML

in_postFDR[] FeatureXMLs after FDR filteringinput file*.featureXML

out Output mzTab with QC informationoutput file*.mzTab

out_cm ConsensusXML with QC information (as metavalues)output file*.consensusXML

out_feat[] FeatureXMLs with QC information (as metavalues)output file*.featureXML

in_contaminants Proteins considered contaminantsinput file*.fasta

in_trafo[] trafoXMLs from MapAlignersinput file*.trafoXML

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

forcefalse Overwrite tool specific checks.true,false

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

+++FragmentMassErrorFragment Mass Error settings

unitauto Unit for mass tolerance. 'auto' uses information from FeatureXMLauto,ppm,da

tolerance20.0 m/z search window for matching peaks in two spectra

+++MS2_id_rateMS2 ID Rate settings

force_no_fdrfalse Forces the metric to run if FDR is missing (accepts all pep_ids as target hits).true,false