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 -- Remove unneeded or verbose table attachments from a qcml file.
Full documentation: http://www.openms.de/doxygen/release/3.4.1/html/TOPP_QCShrinker.html
Version: 3.4.1 May 19 2025, 14:24:34, Revision: 8aec8ec
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 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 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

+QCShrinkerRemove unneeded or verbose table attachments from a qcml file.

version3.4.1 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QCShrinker'

in Input qcml fileinput 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 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