view MapAlignmentEvaluation.xml @ 3:ec62782f6c68 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="1.12.0">
  <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

-in ${param_in}
-gt ${param_gt}
-type ${param_type}
-rt_dev ${param_rt_dev}
-mz_dev ${param_mz_dev}
-int_dev ${param_int_dev}
${param_use_charge}
-threads \${GALAXY_SLOTS:-24} 
</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 true" falsevalue="-use_charge false" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical." help="(-use_charge)"/>
  </inputs>
  <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

@REFERENCES@
</help>
</tool>