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QCCalculator

Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file.

pot. predecessor tools $ \longrightarrow $ QCCalculator $ \longrightarrow $ pot. successor tools
FeatureFinderCentroided QCMerger
XTandemAdapter QCExporter

The calculated quality parameters or data compiled as attachments for easy plotting input include file origin, spectra distribution, aquisition details, ion current stability ( & TIC ), id accuracy statistics and feature statistics. The MS experiments base name is used as name to the qcML element that is comprising all quality parameter values for the given run (including the given downstream analysis data).

Output is in qcML format (see parameter out) which can be viewed directly in a modern browser (chromium, firefox, safari).

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

QCCalculator -- Calculates basic quality parameters from MS experiments and subsequent analysis data as ident
ification or feature detection.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  QCCalculator <options>

Options (mandatory options marked with '*'):
  -in <file>*                  Raw data input file (this is relevant if you want to look at MS1, MS2 and prec
                               ursor peak information) (valid formats: 'mzML')
  -out <file>*                 Your qcML file. (valid formats: 'qcML')
  -id <file>                   Input idXML file containing the identifications. Your identifications will be 
                               exported in an easy-to-read format (valid formats: 'idXML')
  -feature <file>              Feature input file (this is relevant for most QC issues) (valid formats: 'feat
                               ureXML')
  -consensus <file>            Consensus input file (this is only used for charge state deconvoluted output. 
                               Use the consensusXML output form the DeCharger) (valid formats: 'consensusXML'
                               )
  -remove_duplicate_features   This flag should be set, if you work with a set of merged features.
                               
Common UTIL options:
  -ini <file>                  Use the given TOPP INI file
  -threads <n>                 Sets the number of threads allowed to be used by the TOPP tool (default: '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
+QCCalculatorCalculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
version2.3.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'QCCalculator'
in raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)input file*.mzML
out Your qcML file.output file*.qcML
id Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read formatinput file*.idXML
feature feature input file (this is relevant for most QC issues)input file*.featureXML
consensus consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger)input file*.consensusXML
remove_duplicate_featuresfalse This flag should be set, if you work with a set of merged features.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
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13