SpectraFilterNormalizer

Scale intensities per spectrum to either sum to 1 or have a maximum of 1.

pot. predecessor tools	→ SpectraFilter →	pot. successor tools
PeakPickerHiRes		any tool operating on MS peak data (in mzML format)

Normalization is performed for each spectrum independently.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

SpectraFilterNormalizer -- Scale intensities per spectrum to either sum to 1 or have a maximum of 1.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SpectraFilterNormalizer.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:
  SpectraFilterNormalizer <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed description or use the --helphelp option

Options (mandatory options marked with '*'):
  -in <file>*        Input file (valid formats: 'mzML')
  -out <file>*       Output file (valid formats: 'mzML')
                     
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)

The following configuration subsections are valid:
 - algorithm   Algorithm parameter subsection.

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/nightly/html/TOPP_SpectraFilterNormalizer.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+SpectraFilterNormalizerScale intensities per spectrum to either sum to 1 or have a maximum of 1.

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

++1Instance '1' section for 'SpectraFilterNormalizer'

in input fileinput file*.mzML

out output fileoutput file*.mzML

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

+++algorithmAlgorithm parameter subsection.

methodto_one Normalize via dividing by TIC ('to_TIC') per spectrum (i.e. all peaks sum to 1) or normalize to max. intensity to one ('to_one') per spectrum.to_one, to_TIC