Repairs MALDI experiments which were spotted line by line.

The command line parameters of this tool are:

DeMeanderize -- Orders the spectra of MALDI spotting plates correctly.
Full documentation: http://www.openms.de/doxygen/release/3.1.0/html/TOPP_DeMeanderize.html
Version: 3.1.0 Oct 18 2023, 10:27:18, Revision: 17a07f8
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:
  DeMeanderize <options>

Options (mandatory options marked with '*'):
  -in <mzML-file>*              Input experiment file, containing the wrongly sorted spectra. (valid formats:
                                 'mzML')
  -out <mzML-file>*             Output experiment file with correctly sorted spectra. (valid formats: 'mzML')

  -num_spots_per_row <integer>  Number of spots in one column, until next row is spotted. (default: '48') 
                                (min: '1')
                                
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

+DeMeanderizeOrders the spectra of MALDI spotting plates correctly.

version3.1.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'DeMeanderize'

in Input experiment file, containing the wrongly sorted spectra.input file*.mzML

out Output experiment file with correctly sorted spectra.output file*.mzML

num_spots_per_row48 Number of spots in one column, until next row is spotted.1:∞

RT_distance1.0 RT distance between two spots which is used to calculated pseudo RT.0.0:∞

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