OpenMS
QCExporter

Will extract several quality parameter from several run/sets from a qcML file into a tabular (text) format - counterpart to QCImporter.

pot. predecessor tools → QCExporter → pot. successor tools
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QCEmbedder

The data contained as values of the qp of a qcML file at in can be exported in tabluar (csv) format.

  • names The name of the target runs or sets to be exported from. If empty, from all will be exported.
  • mapping The mapping of the exported table's headers to the according qp cvs. The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported.

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

The command line parameters of this tool are:

QCExporter -- Will extract several qp from several run/sets in a tabular format.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCExporter.html
Version: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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 QCExporter:
 + 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:
  QCExporter <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input qcml file (valid formats: 'qcML')
  -names <names>     The name of the target runs or sets to be exported from. If empty, from all will be expo
                     rted.
  -mapping <file>*   The mapping of the exported table's headers to the according qp cvs. The first row is 
                     considered containing the headers as for the exported the table. The second row is consi
                     dered the according qp cv accessions of the qp to be exported. (valid formats: 'csv')
  -out_csv <file>*   Output csv formatted quality parameter. (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
+QCExporterWill extract several qp from several run/sets in a tabular format.
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'QCExporter'
in Input qcml fileinput file*.qcML
names[] The name of the target runs or sets to be exported from. If empty, from all will be exported.
mapping The mapping of the exported table's headers to the according qp cvs. The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported.input file*.csv
out_csv Output csv formatted quality parameter.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