<?xml version="1.0" encoding="UTF-8"?>
  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
  <!--Proposed Tool Section: [Utilities]-->
  <tool id="DeMeanderize" name="DeMeanderize" version="2.0.0">
    <description>Orders the spectra of MALDI spotting plates correctly.</description>
    <macros>
      <token name="@EXECUTABLE@">DeMeanderize</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>DeMeanderize

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_num_spots_per_row:
  -num_spots_per_row $param_num_spots_per_row
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_RT_distance:
  -RT_distance $adv_opts.param_RT_distance
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="Input experiment file, containing the wrongly sorted spectra" name="param_in" optional="False" type="data"/>
      <param help="(-num_spots_per_row) " label="Number of spots in one column, until next row is spotted" min="1" name="param_num_spots_per_row" optional="True" type="integer" value="48"/>
      <expand macro="advanced_options">
        <param help="(-RT_distance) " label="RT distance between two spots which is used to calculated pseudo RT" min="0.0" name="param_RT_distance" optional="True" type="float" value="1.0"/>
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="mzml" name="param_out"/>
    </outputs>
    <help>Orders the spectra of MALDI spotting plates correctly.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DeMeanderize.html</help>
  </tool>