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/release/3.0.0/html/UTILS_OpenSwathFileSplitter.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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.

Usage:
  OpenSwathFileSplitter <options>

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

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

version3.0.0 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