OpenMS: SpectraFilterBernNorm

Filters the top Peaks in the given spectra according to a given schema/thresholdset

pot. predecessor tools	$\longrightarrow$ SpectraFilter $\longrightarrow$	pot. successor tools
PeakPickerWavelet	$\longrightarrow$ SpectraFilter $\longrightarrow$	any tool operating on MS peak data (in mzML format)

The command line parameters of this tool are:

SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra.
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  SpectraFilterBernNorm <options>

This tool has algoritm parameters which can only be used via an INI file and are not accessible from the command line!

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.
Have a look at OpenMS documentation for more information.

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+SpectraFilterBernNormApplies thresholdfilter to peak spectra.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SpectraFilterBernNorm'

in input file input file*.mzML

out output file output 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

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

+++algorithmAlgorithm parameter subsection.

C128 C1 value of the normalization.

C2400 C2 value of the normalization.

threshold0.1 Threshold of the Bern et al. normalization.

For the parameters of the algorithm section see the class documentation:
OpenMS::BernNorm