QCEmbedder

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:

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

Usage:
  QCEmbedder <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input qcml file (valid formats: 'qcML')
  -qp <string>*      Target attachment table.
  -qp_acc <string>   The accession number of the given qp, only needed if qp is not yet contained in the run/
                     set.
  -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')
  -plot <file>*      Plot file to be added to target quality parameter. (Plot file generated from csv output.
                     ) (valid formats: 'PNG')
  -table <file>      Table file that will be added as attachment to the given qc. (valid formats: 'csv')
  -out <file>*       Output extended/reduced qcML file (valid formats: 'qcML')
                     
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

+QCEmbedderproduces qcml files

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

++1Instance '1' section for 'QCEmbedder'

in Input qcml fileinput file*.qcML

qp Target attachment table.

qp_acc The accession number of the given qp, only needed if qp is not yet contained in the run/set.

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

plot Plot file to be added to target quality parameter. (Plot file generated from csv output.)input file*.PNG

table Table file that will be added as attachment to the given qc.input file*.csv

out Output extended/reduced qcML fileoutput file*.qcML

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