QCExporter

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:

QCExporter -- produces qcml files
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  QCExporter <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input qcml file (valid formats: 'qcML')
  -qp <choice>*      Target attachment table. (valid: 'precursor tables', 'charge tables', 'total ion current
                     tables', 'delta ppm tables', 'feature tables', 'set id')
  -name <string>     The name of the target run or set that contains the requested quality parameter.
  -run <file>        The file from which the name of the target run that contains the requested quality param
                     eter is taken. This overrides the name parameter! (valid formats: 'mzML')
  -out_csv <file>*   Output csv formated quality parameter or extended qcML file (valid formats: 'csv')
                     
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

+QCExporterproduces qcml files

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

++1Instance '1' section for 'QCExporter'

in Input qcml fileinput file*.qcML

qp Target attachment table.precursor tables,charge tables,total ion current tables,delta ppm tables,feature tables,set id

name The name of the target run or set that contains the requested quality parameter.

run The file from which the name of the target run that contains the requested quality parameter is taken. This overrides the name parameter!input file*.mzML

out_csv Output csv formated quality parameter or extended qcML fileoutput file*.csv

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