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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FFEval" name="FFEval" version="1.12.0">
  <description>Evaluation tool for feature detection algorithms.</description>
  <macros>
    <token name="@EXECUTABLE@">FFEval</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FFEval

-in ${param_in}
-truth ${param_truth}
-rt_tol ${param_rt_tol}
-rt_tol_abs ${param_rt_tol_abs}
-mz_tol ${param_mz_tol}
-out ${param_out}
-abort_reasons ${param_abort_reasons}
-out_roc ${param_out_roc}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" label="Feature input file, which contains the data to be tested against the truth file." help="(-in)"/>
    <param name="param_truth" type="data" format="featureXML" optional="False" label="Truth feature file that defines what features should be found." help="(-truth)"/>
    <param name="param_rt_tol" type="float" min="0.0" optional="True" value="0.3" label="Allowed tolerance of RT relative to average feature RT span." help="(-rt_tol)"/>
    <param name="param_rt_tol_abs" type="float" min="-1.0" optional="True" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)." help="(-rt_tol_abs)"/>
    <param name="param_mz_tol" type="float" min="0.0" optional="True" value="0.25" label="Allowed tolerance in m/z (is divided by charge)." help="(-mz_tol)"/>
    <param name="param_abort_reasons" type="data" format="featureXML" optional="True" label="Feature file containing seeds with abort reasons." help="(-abort_reasons)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Feature output file. If given, an annotated input file is written." format="featureXML"/>
    <data name="param_out_roc" label="If given, a ROC curve file is created (ROC points based on intensity threshold)" format="tabular"/>
  </outputs>
  <help>**What it does**

Evaluation tool for feature detection algorithms.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html

@REFERENCES@
</help>
</tool>