A tool for splitting a single SWATH / DIA file into a set of files, each containing one SWATH window (plus one file for the MS1 survey scans).

Will use the input SWATH / DIA file to generate one output file containing the MS1 survey scans and n individual files for each SWATH / DIA window in the input file. The number of windows is read from the input file itself.

The command line parameters of this tool are:

OpenSwathFileSplitter -- Splits SWATH files into n files, each containing one window.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathFileSplitter.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.

Usage:
  OpenSwathFileSplitter <options>

Options (mandatory options marked with '*'):
  -in <files>*       Input file (SWATH/DIA file) (valid formats: 'mzML', 'mzXML')
                     
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.

+OpenSwathFileSplitterSplits SWATH files into n files, each containing one window.

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

++1Instance '1' section for 'OpenSwathFileSplitter'

in Input file (SWATH/DIA file)input file*.mzML, *.mzXML

outputDirectory./ Output file prefixoutput prefix

out_qc Optional QC meta data (charge distribution in MS1). Only works with mzML input files.output file*.json

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