OpenMS
QCExtractor

Extracts a table attachment of a given quality parameter from a qcML file as tabular (text) format.

pot. predecessor tools → QCExtractor → pot. successor tools
QCEmbedder
QCShrinker

If there is a table attached to a given qp that is needed as a single file, e.g. for easy input to plotting software, this can be extracted to a tabular (text) format.

  • qp defines the qp name to which the table is attached;
  • 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.
  • 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.
  • set/run if the target qp is contained in a set, this has to be set here;

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.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCExtractor.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
To cite QCExtractor:
 + Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P,  Martens, L. qcML: An Exchange 
   Format for Quality Control Metrics from Mass Spectrometry Experiments. Molecular & Cellular Proteomics 
   2014; 13(8). doi:10.1074/mcp.M113.035907.

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 TOPP 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.
version3.2.0-pre-nightly-2024-07-21 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
forcefalse Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false