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.
Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
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.

version2.4.0 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 path to store the split files

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 Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false