OpenMS  2.5.0
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/documentation/UTILS_DeMeanderize.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:

  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 UTIL 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.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND 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 Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false