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QCExtractor

Extracts a table attachment to a given qc parameter.

pot. predecessor tools $ \longrightarrow $ QCExtractor $ \longrightarrow $ pot. successor tools
QCEmbedder
QCShrinker

If there is a table attached to a qp that is needed as a single file. The qcml file to extract from is given with in.

Output is in csv format (see parameter out_csv) which can be easily parsed by many programs.

The command line parameters of this tool are:

QCExtractor -- Extracts a table attachment to a given qc parameter.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  QCExtractor <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input qcml file (valid formats: 'qcML')
  -qp <string>*      Target attachment qp.
  -run <file>        The file that defined the run under which the qp for the attachment is aggregated as 
                     mzML file. The file is only used to extract the run name from the file name. (valid form
                     ats: 'mzML')
  -name <string>     If no file for the run was given (or if the target qp is contained in a set), at least 
                     a name of the target run/set containing the the qp for the attachment has to be given.
  -out_csv <file>*   Output csv formatted table. (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
+QCExtractorExtracts a table attachment to a given qc parameter.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'QCExtractor'
in Input qcml fileinput file*.qcML
qp Target attachment qp.
run The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name.input file*.mzML
name If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given.
out_csv Output csv formatted table.output 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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5