MzMLSplitter

Splits an mzML file into multiple parts

This utility will split an input mzML file into N parts, with an approximately equal number of spectra and chromatograms in each part. N is set by the parameter parts; optionally only spectra (parameter no_chrom) or only chromatograms (parameter no_spec) can be transferred to the output.

Alternatively to setting the number of parts directly, a target maximum file size for the parts can be specified (parameters size and unit). The number of parts is then calculated by dividing the original file size by the target and rounding up. Note that the resulting parts may actually be bigger than the target size (due to meta data that is included in every part) or that more parts than necessary may be produced (if spectra or chromatograms are removed via no_spec/no_chrom).

This tool cannot be used as part of a TOPPAS workflow, because the number of output files is variable.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

MzMLSplitter -- Splits an mzML file into multiple parts
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MzMLSplitter.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  MzMLSplitter <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file (valid formats: 'mzML')
  -out <prefix>      Prefix for output files ('_part1of2.mzML' etc. will be appended; default: same as 'in' without the file extension)
  -parts <num>       Number of parts to split into (takes precedence over 'size' if set) (default: '1') (min: '1')
  -size <num>        Approximate upper limit for resulting file sizes (in 'unit') (default: '0') (min: '0')
  -unit <choice>     Unit for 'size' (base 1024) (default: 'MB') (valid: 'KB', 'MB', 'GB')
  -no_chrom          Remove chromatograms, keep only spectra.
  -no_spec           Remove spectra, keep only chromatograms.
                     
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

+MzMLSplitterSplits an mzML file into multiple parts

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MzMLSplitter'

in Input fileinput file*.mzML

out Prefix for output files ('_part1of2.mzML' etc. will be appended; default: same as 'in' without the file extension)output prefix

parts1 Number of parts to split into (takes precedence over 'size' if set)1:∞

size0 Approximate upper limit for resulting file sizes (in 'unit')0:∞

unitMB Unit for 'size' (base 1024)KB, MB, GB

no_chromfalse Remove chromatograms, keep only spectra.true, false

no_specfalse Remove spectra, keep only chromatograms.true, false

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