OpenMS
DeMeanderize

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/nightly/html/TOPP_DeMeanderize.html
Version: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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.
version3.2.0-pre-nightly-2024-07-19 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