OpenMS: NoiseFilterGaussian

| OpenMS 2.5.0

NoiseFilterGaussian

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

pot. predecessor tools | NoiseFilterGaussian | 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).

    Full documentation: http://www.openms.de/documentation/TOPP_NoiseFilterGaussian.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      NoiseFilterGaussian <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 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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/TOPP_NoiseFilterGaussian.html

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).
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND 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
processOption inmemory Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory firstinmemory,lowmemory
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command linetrue,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
gaussian_width 0.2 Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z).
ppm_tolerance 10.0 Gaussian width, depending on the m/z position.
The higher the value, the wider the peak and therefore the wider the gaussian.
use_ppm_tolerance false 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