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<?xml version='1.0' encoding='UTF-8'?>
<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="1.12.0">
  <description>Compute confidence scores for OpenSwath results</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathConfidenceScoring

-in ${param_in}
-lib ${param_lib}
-out ${param_out}
-trafo ${param_trafo}
-decoys ${param_decoys}
-transitions ${param_transitions}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -GLM:intercept ${adv_opts.param_intercept}
    -GLM:delta_rt ${adv_opts.param_delta_rt}
    -GLM:dist_int ${adv_opts.param_dist_int}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" label="Input file (OpenSwath results)" help="(-in)"/>
    <param name="param_lib" type="data" format="" optional="False" label="Assay library" help="(-lib)"/>
    <param name="param_trafo" type="data" format="" optional="True" label="Retention time transformation" help="(-trafo)"/>
    <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys)"/>
    <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help="(-transitions)"/>
    <expand macro="advanced_options">
      <param name="param_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept)"/>
      <param name="param_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt)"/>
      <param name="param_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file (results with confidence scores)" format="featureXML"/>
  </outputs>
  <help>**What it does**

Compute confidence scores for OpenSwath results


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

@REFERENCES@
</help>
</tool>