| OpenMS 2.5.0

Resampler

Resampler can be used to transform an LC/MS map into a resampled map.

pot. predecessor tools | Resampler | pot. successor tools
- | NoiseFilterSGolay

When writing an peak file, all spectra are resampled with a new sampling rate. The number of spectra does not change.

The command line parameters of this tool are:

    Resampler -- Transforms an LC/MS map into a resampled map or a PNG image.

    Full documentation: http://www.openms.de/documentation/TOPP_Resampler.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:

      Resampler <options>

    Options (mandatory options marked with '*'):

      -in <file>*                      Input file  (valid formats: 'mzML')

      -out <file>*                     Output file in mzML format (valid formats: 'mzML')

      -sampling_rate <rate>            New sampling rate in m/z dimension (in Th unless ppm flag is set) (default

                                       : '0.1' min: '0.0')

      -ppm                             Sampling_rate is given in ppm

      -align_sampling                  Ensures that sampling is performed equally across the map (same raster is

                                       used for all spectra)

      -min_int_cutoff <min intensity>  Intensity cutoff for peaks to be stored in output spectrum (only peaks

                                       above this cutoff will be stored, -1 means store all data) (default: '-1.0

                                       ')

    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)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+Resampler Transforms an LC/MS map into a resampled map or a PNG image.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'Resampler'
in input file input file*.mzML
out output file in mzML format output file*.mzML
sampling_rate 0.1 New sampling rate in m/z dimension (in Th unless ppm flag is set)0.0:∞
ppm false sampling_rate is given in ppm true,false
align_sampling false Ensures that sampling is performed equally across the map (same raster is used for all spectra)true,false
min_int_cutoff-1.0 Intensity cutoff for peaks to be stored in output spectrum (only peaks above this cutoff will be stored, -1 means store all data)
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 line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false