<?xml version='1.0' encoding='UTF-8'?>
<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="stdio"/>
  <expand macro="requirements"/>
  <command>MapAlignmentEvaluation

#if $param_in:
  -in $param_in
#end if
#if $param_gt:
  -gt $param_gt
#end if
#if $param_type:
  -type
  #if " " in str($param_type):
    "$param_type"
  #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 name="param_in" type="data" format="consensusxml" optional="False" label="input file: tool" help="(-in) "/>
    <param name="param_gt" type="data" format="consensusxml" optional="False" label="input file: ground truth" help="(-gt) "/>
    <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type) ">
      <option value="precision">precision</option>
      <option value="recall">recall</option>
      <option value="F1">F1</option>
    </param>
    <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev) "/>
    <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev) "/>
    <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev) "/>
    <param name="param_use_charge" type="boolean" truevalue="-use_charge" falsevalue="" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical" help="(-use_charge) "/>
    <expand macro="advanced_options">
      <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_stdout" format="text" label="Output from stdout"/>
  </outputs>
  <help>**What it does**

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