<?xml version='1.0' encoding='UTF-8'?>
<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="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 name="param_in" type="data" format="mzml" optional="False" label="Input experiment file, containing the wrongly sorted spectra" help="(-in) "/>
    <param name="param_num_spots_per_row" type="integer" min="1" optional="True" value="48" label="Number of spots in one column, until next row is spotted" help="(-num_spots_per_row) "/>
    <expand macro="advanced_options">
      <param name="param_RT_distance" type="float" min="0.0" optional="True" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help="(-RT_distance) "/>
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
  </outputs>
  <help>**What it does**

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>
  <expand macro="references"/>
</tool>