<?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: [Map Alignment]-->
  <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.0.0">
    <description>Groups corresponding isotope-labeled features in a feature map.</description>
    <macros>
      <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>FeatureLinkerLabeled

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_rt_estimate:
  -algorithm:rt_estimate
#end if
#if $param_algorithm_rt_pair_dist:
  -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
#end if
#if $param_algorithm_rt_dev_low:
  -algorithm:rt_dev_low $param_algorithm_rt_dev_low
#end if
#if $param_algorithm_rt_dev_high:
  -algorithm:rt_dev_high $param_algorithm_rt_dev_high
#end if

#if $rep_param_algorithm_mz_pair_dists:
-algorithm:mz_pair_dists
  #for token in $rep_param_algorithm_mz_pair_dists:
    #if &quot; &quot; in str(token):
      &quot;$token.param_algorithm_mz_pair_dists&quot;
    #else
      $token.param_algorithm_mz_pair_dists
    #end if
  #end for
#end if
#if $param_algorithm_mz_dev:
  -algorithm:mz_dev $param_algorithm_mz_dev
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_mrm:
  -algorithm:mrm
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
      <param checked="true" falsevalue="" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" name="param_algorithm_rt_estimate" optional="True" truevalue="-algorithm:rt_estimate" type="boolean"/>
      <param help="(-rt_pair_dist) " label="optimal pair distance in RT [sec] from light to heavy feature" name="param_algorithm_rt_pair_dist" type="float" value="-20.0"/>
      <param help="(-rt_dev_low) " label="maximum allowed deviation below optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_low" optional="True" type="float" value="15.0"/>
      <param help="(-rt_dev_high) " label="maximum allowed deviation above optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_high" optional="True" type="float" value="15.0"/>
      <repeat max="1" min="0" name="rep_param_algorithm_mz_pair_dists" title="param_algorithm_mz_pair_dists">
        <param help="(-mz_pair_dists) by division through charge)" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." name="param_algorithm_mz_pair_dists" size="30" type="text" value="4.0">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param help="(-mz_dev) " label="maximum allowed deviation from optimal m/z distance" min="0.0" name="param_algorithm_mz_dev" optional="True" type="float" value="0.05"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param checked="false" falsevalue="" help="(-mrm) " label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" name="param_algorithm_mrm" optional="True" truevalue="-algorithm:mrm" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="consensusxml" name="param_out"/>
    </outputs>
    <help>Groups corresponding isotope-labeled features in a feature map.


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