| 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
+DeMeanderize Orders the spectra of MALDI spotting plates correctly.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '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_row 48 Number of spots in one column, until next row is spotted.1:∞
RT_distance 1.0 RT distance between two spots which is used to calculated pseudo RT.0.0:∞
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