OpenMS  2.5.0
SpectraFilterParentPeakMower

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

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

  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.
version2.5.0-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)
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 Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameter subsection.
window_size2.0 The size of the m/z window where the peaks are removed, +/- window_size.
default_charge2 If the precursor has no charge set, the default charge is assumed.
clean_all_charge_states1 Set to 1 if precursor ions of all possible charge states should be removed.
consider_NH3_loss1 Whether NH3 loss peaks from the precursor should be removed.
consider_H2O_loss1 Whether H2O loss peaks from the precursor should be removed.
reduce_by_factor0 Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0).
factor1000.0 Factor which is used to reduce the intensities if 'reduce_by_factor' is selected.
set_to_zero1 Reduce the intensities of the precursor and related ions to zero.