<?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: [Targeted Experiments]-->
<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.2.0">
  <description>Compute confidence scores for OpenSwath results</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathConfidenceScoring

#if $param_in:
  -in $param_in
#end if
#if $param_lib:
  -lib $param_lib
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_trafo:
  -trafo $param_trafo
#end if
#if $param_decoys:
  -decoys $param_decoys
#end if
#if $param_transitions:
  -transitions $param_transitions
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_GLM_intercept:
  -GLM:intercept $adv_opts.param_GLM_intercept
#end if
    #if $adv_opts.param_GLM_delta_rt:
  -GLM:delta_rt $adv_opts.param_GLM_delta_rt
#end if
    #if $adv_opts.param_GLM_dist_int:
  -GLM:dist_int $adv_opts.param_GLM_dist_int
#end if
#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="traml" optional="False" label="Assay library" help="(-lib) "/>
    <param name="param_trafo" type="data" format="trafoxml" 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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/>
      <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/>
      <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Compute confidence scores for OpenSwath results


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