| OpenMS 2.5.0

QualityControl

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 | QualityControl | 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-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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
+QualityControl Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '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 filtering input file*.featureXML
out Output mzTab with QC information output 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 contaminants input file*.fasta
in_trafo[] trafoXMLs from MapAligners input file*.trafoXML
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++FragmentMassError Fragment Mass Error settings
unit auto Unit for mass tolerance. 'auto' uses information from FeatureXML auto,ppm,da
tolerance 20.0 m/z search window for matching peaks in two spectra
+++MS2_id_rate MS2 ID Rate settings
force_no_fdr false Forces the metric to run if FDR is missing (accepts all pep_ids as target hits).true,false