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NoiseFilterGaussian

Executes a Gaussian filter to reduce the noise in an MS experiment.

pot. predecessor tools $ \longrightarrow $ NoiseFilterGaussian $ \longrightarrow $ pot. successor tools
FileConverter PeakPickerWavelet
Resampler PeakPickerHiRes
BaselineFilter

The Gaussian filter is a peak area preserving low-pass filter and is characterized by narrow bandwidths, sharp cutoffs, and low passband ripple.

Note
The Gaussian filter works for uniform as well as for non-uniform data.

The command line parameters of this tool are:

NoiseFilterGaussian -- Removes noise from profile spectra by using Gaussian filter (on uniform as well as 
non-uniform data).
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  NoiseFilterGaussian <options>

This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.

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

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 the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+NoiseFilterGaussianRemoves noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'NoiseFilterGaussian'
in input raw data file input file*.mzML
out output raw data 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 parameters section
gaussian_width0.2 Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z).
ppm_tolerance10 Gaussian width, depending on the m/z position.
The higher the value, the wider the peak and therefore the wider the gaussian.
use_ppm_tolerancefalse If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower.true,false

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5