QCMerger

Merges two qcml files together.

pot. predecessor tools	→ QCCalculator →	pot. successor tools
QCCalculator
		QCShrinker

The two or more given files (see parameter in) are merged. If a run/set exisits in several files, the quality parameters of these are merged as well. Several runs from qcml files can be comprised in a set.

• setname If the runs of the given input files are to be comprised in a set, this will be the name of the set.

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:

QCMerger -- Merges two qcml files together.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCMerger.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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 QCMerger:
 + 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:
  QCMerger <options>

Options (mandatory options marked with '*'):
  -in <files>*       List of qcml files to be merged. (valid formats: 'qcML')
  -out <file>*       Output extended/reduced qcML file (valid formats: 'qcML')
  -setname <string>  Use only when all given qcml files belong to one set, which will be held under the given
                      name.
                     
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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

• Name The identifier used in configuration files and on the command line.
• Default value The value used if the parameter is not explicitly specified.
• Description A short explanation describing the purpose and behavior of the parameter.
• Tags Additional metadata associated with the parameter.
• Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+QCMergerMerges two qcml files together.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QCMerger'

in[] List of qcml files to be merged.input file*.qcML

out Output extended/reduced qcML fileoutput file*.qcML

setname Use only when all given qcml files belong to one set, which will be held under the given name.

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