| OpenMS 2.5.0

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/documentation/UTILS_QCImporter.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 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 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
+QCImporter Imports tables with quality control parameters into qcml files.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'QCImporter'
in Input qcml file input 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 file output file*.qcML
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