Normalizes intensity of peak spectra.

pot. predecessor tools	$\longrightarrow$ SpectraFilter $\longrightarrow$	pot. successor tools
PeakPickerWavelet	$\longrightarrow$ SpectraFilter $\longrightarrow$	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:

SpectraFilterNormalizer -- Normalizes intensity of peak spectra.
Full documentation: http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html
Version: 2.8.0 Feb 22 2022, 11:52:07, Revision: d203985
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:
SpectraFilterNormalizer <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion 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/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+SpectraFilterNormalizerNormalizes intensity of peak spectra.

version2.8.0 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 or normalize to max. intensity of one ('to_one') per spectrum.to_one,to_TIC