| OpenMS 2.5.0

QCShrinker

This application is used to remove extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report.

pot. predecessor tools | QCShrinker | pot. successor tools
QCMerger
...

If there is a lot of verbose or deprecated information in the given qcml file at `in` that can be purged.

- `qp_accessions` A list of cv accessions that should be removed. If empty, the usual suspects will be removed.
- `run` the file that defined the run under which the qp for the attachment is aggregated as MZML file. The file is only used to extract the run name from the file name;
- `name` if no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given;

Output is in qcML format (see parameter `out`) which can be viewed directly in a modern browser (chromium, firefox, safari).

The command line parameters of this tool are:

    QCShrinker -- This application is used to remove the verbose table attachments from a qcml file that are not

    needed anymore, e.g. for a final report.

    Full documentation: http://www.openms.de/documentation/UTILS_QCShrinker.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 QCShrinker:

      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:

      QCShrinker <options>

    Options (mandatory options marked with '*'):

      -in <file>*             Input qcml file (valid formats: 'qcML')

      -qp_accessions <names>  A list of cv accessions that should be removed. If empty, the usual suspects will

                              be removed!

      -name <string>          The name of the target run or set that contains the requested quality parameter.

      -run <file>             The file from which the name of the target run that contains the requested quality

                              parameter is taken. This overrides the name parameter! (valid formats: 'mzML')

      -out <file>*            Output extended/reduced 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
+QCShrinker This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'QCShrinker'
in Input qcml file input file*.qcML
qp_accessions[] A list of cv accessions that should be removed. If empty, the usual suspects will be removed!
name The name of the target run or set that contains the requested quality parameter.
run The file from which the name of the target run that contains the requested quality parameter is taken. This overrides the name parameter!input file*.mzML
out Output extended/reduced 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