OpenMS: SpectraFilterParentPeakMower

| OpenMS 2.5.0

SpectraFilterParentPeakMower

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

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

The command line parameters of this tool are:

    SpectraFilterParentPeakMower -- Applies thresholdfilter to peak spectra.
    Full documentation: http://www.openms.de/documentation/TOPP_SpectraFilterParentPeakMower.html
    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep  8 2020, 18:59:55, 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:
      SpectraFilterParentPeakMower <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/documentation/TOPP_SpectraFilterParentPeakMower.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+SpectraFilterParentPeakMowerApplies thresholdfilter to peak spectra.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1Instance '1' section for 'SpectraFilterParentPeakMower'
in input file input file*.mzML
out output file output file*.mzML
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 parameter subsection.
window_size 2.0 The size of the m/z window where the peaks are removed, +/- window_size.
default_charge 2 If the precursor has no charge set, the default charge is assumed.
clean_all_charge_states 1 Set to 1 if precursor ions of all possible charge states should be removed.
consider_NH3_loss 1 Whether NH3 loss peaks from the precursor should be removed.
consider_H2O_loss 1 Whether H2O loss peaks from the precursor should be removed.
reduce_by_factor 0 Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0).
factor 1000.0 Factor which is used to reduce the intensities if 'reduce_by_factor' is selected.
set_to_zero 1 Reduce the intensities of the precursor and related ions to zero.