QCCalculator

This application is used to provide data export from raw, id and feature data files generated via TOPP pipelines. It is intended to provide tables that can be read into R where QC metrics will be calculated.

The command line parameters of this tool are:

QCCalculator -- produces table data dedicted for R import. These data is produced based on mzML, featureXMl and/ or idXML files
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

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.
  -MS1                         This flag should be set, if you want to work with MS1 stats.
  -MS2                         This flag should be set, if you want to work with MS2 stats.
                               
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

+QCCalculatorproduces table data dedicted for R import. These data is produced based on mzML, featureXMl and/ or idXML files

version1.10.0 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

MS1false This flag should be set, if you want to work with MS1 stats.true,false

MS2false This flag should be set, if you want to work with MS2 stats.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