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
?	→ QCExporter →
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:

stty: 'standard input': Inappropriate ioctl for device

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: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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 exported.
  -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 considered 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.

version3.4.0-pre-nightly-2024-12-16 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