<?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="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.0.0">
    <description>Evaluates alignment results against a ground truth.</description>
    <macros>
      <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>MapAlignmentEvaluation

#if $param_in:
  -in $param_in
#end if
#if $param_gt:
  -gt $param_gt
#end if
#if $param_type:
  -type
  #if &quot; &quot; in str($param_type):
    &quot;$param_type&quot;
  #else
    $param_type
  #end if
#end if
#if $param_rt_dev:
  -rt_dev $param_rt_dev
#end if
#if $param_mz_dev:
  -mz_dev $param_mz_dev
#end if
#if $param_int_dev:
  -int_dev $param_int_dev
#end if
#if $param_use_charge:
  -use_charge
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
&gt; $param_stdout
</command>
    <inputs>
      <param format="consensusxml" help="(-in) " label="input file: tool" name="param_in" optional="False" type="data"/>
      <param format="consensusxml" help="(-gt) " label="input file: ground truth" name="param_gt" optional="False" type="data"/>
      <param help="(-type) " label="Caap Evaluation type" name="param_type" optional="False" type="select">
        <option value="precision">precision</option>
        <option value="recall">recall</option>
        <option value="F1">F1</option>
      </param>
      <param help="(-rt_dev) " label="Maximum allowed deviation of the retention time" name="param_rt_dev" type="float" value="0.1"/>
      <param help="(-mz_dev) " label="Maximum allowed deviation of m/z" name="param_mz_dev" type="float" value="0.1"/>
      <param help="(-int_dev) " label="Maximum allowed deviation of Intensity" name="param_int_dev" type="float" value="100.0"/>
      <param checked="false" falsevalue="" help="(-use_charge) " label="Use charge criterion when assesing if two features are identical" name="param_use_charge" optional="True" truevalue="-use_charge" type="boolean"/>
      <expand macro="advanced_options">
        <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="text" label="Output from stdout" name="param_stdout"/>
    </outputs>
    <help>Evaluates alignment results against a ground truth.


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