OpenMS
QCImporter

Will import several quality parameter from a tabular (text) format into a qcML file - counterpart to QCExporter.

pot. predecessor tools → QCEmbedder → pot. successor tools
QCExporter QCMerger
XTandemAdapter QCShrinker

If there is additional data from external tools in tabular format containing additional quality parameter (qp) to runs or sets, or even new runs, these can be imported into the qcML file. For an example see the examples in the share directory.

  • table The table containing the additional qp values in the columns. First row is considered containing the header. The target run or set names/ids are indicated by column "raw data file", so each row after the header will contain the values of qps for that run.
  • mapping The mapping of the table header to the according qp cvs, also in csv format. The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions.

The command line parameters of this tool are:

QCImporter -- Imports tables with quality control parameters into qcml files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCImporter.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 QCImporter:
 + 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:
  QCImporter <options>

Options (mandatory options marked with '*'):
  -in <file>         Input qcml file (valid formats: 'qcML')
  -table <file>*     The table containing the additional qp values in the columns. First row is considered 
                     containing the header. The target run or set names/ids are indicated by column "raw data
                      file", so each row after the header will contain the values of qps for that run. (csv 
                     without "!) (valid formats: 'csv')
  -mapping <file>*   The mapping of the table header to the according qp cvs, also in csv format. The first 
                     row is considered containing the headers as in the table. The second row is considered 
                     the according qp cv accessions. (csv without "!) (valid formats: 'csv')
  -out <file>*       Output extended qcML file (valid formats: 'qcML')
                     
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
+QCImporterImports tables with quality control parameters into qcml files.
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'QCImporter'
in Input qcml fileinput file*.qcML
table The table containing the additional qp values in the columns. First row is considered containing the header. The target run or set names/ids are indicated by column "raw data file", so each row after the header will contain the values of qps for that run. (csv without "!)input file*.csv
mapping The mapping of the table header to the according qp cvs, also in csv format. The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without "!)input file*.csv
out Output extended qcML fileoutput file*.qcML
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