| OpenMS 2.5.0

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/documentation/UTILS_QCExporter.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    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 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
+QCExporter Will extract several qp from several run/sets in a tabular format.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'QCExporter'
in Input qcml file input 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)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false