OpenMS
OpenSwathFileSplitter

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: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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
+OpenSwathFileSplitterSplits SWATH files into n files, each containing one window.
version3.2.0-pre-nightly-2024-07-19 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