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

pot. predecessor tools	→ Resampler →	pot. successor tools
-	→ Resampler →	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:

stty: 'standard input': Inappropriate ioctl for device

Resampler -- Transforms an LC/MS map into a resampled map or a PNG image.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_Resampler.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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

+ResamplerTransforms an LC/MS map into a resampled map or a PNG image.

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'Resampler'

in input file input file*.mzML

out output file in mzML formatoutput file*.mzML

sampling_rate0.1 New sampling rate in m/z dimension (in Th unless ppm flag is set)0.0:∞

ppmfalse sampling_rate is given in ppmtrue, false

align_samplingfalse 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)

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 Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false