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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MRMPairFinder" name="MRMPairFinder" version="1.12.0">
  <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
  <macros>
    <token name="@EXECUTABLE@">MRMPairFinder</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MRMPairFinder

-in ${param_in}
-pair_in ${param_pair_in}
-out ${param_out}
-feature_out ${param_feature_out}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -mass_tolerance ${adv_opts.param_mass_tolerance}
    -RT_tolerance ${adv_opts.param_RT_tolerance}
    -RT_pair_tolerance ${adv_opts.param_RT_pair_tolerance}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" label="Input featureXML file containing the features of the MRM experiment spectra." help="(-in)"/>
    <param name="param_pair_in" type="data" format="tabular" optional="False" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help="(-pair_in)"/>
    <expand macro="advanced_options">
      <param name="param_mass_tolerance" type="float" min="0.0" optional="True" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features." help="(-mass_tolerance)"/>
      <param name="param_RT_tolerance" type="float" min="0.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file." help="(-RT_tolerance)"/>
      <param name="param_RT_pair_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have." help="(-RT_pair_tolerance)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output consensusXML file were the pairs of the features will be written to." format="consensusXML"/>
    <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/>
  </outputs>
  <help>**What it does**

Util which can be used to evaluate labeled pair ratios on MRM features.


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

@REFERENCES@
</help>
</tool>