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<?xml version='1.0' encoding='UTF-8'?>
<tool id="ERPairFinder" name="ERPairFinder" version="1.12.0">
  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
  <macros>
    <token name="@EXECUTABLE@">ERPairFinder</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ERPairFinder

-in ${param_in}
-pair_in ${param_pair_in}
-out ${param_out}
-feature_out ${param_feature_out}
-precursor_mass_tolerance ${param_precursor_mass_tolerance}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -RT_tolerance ${adv_opts.param_RT_tolerance}
    -max_charge ${adv_opts.param_max_charge}
    -intensity_threshold ${adv_opts.param_intensity_threshold}
    -max_isotope ${adv_opts.param_max_isotope}
    -expansion_range ${adv_opts.param_expansion_range}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file containing the ER spectra." help="(-in)"/>
    <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in)"/>
    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" 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="(-precursor_mass_tolerance)"/>
    <expand macro="advanced_options">
      <param name="param_RT_tolerance" type="float" min="1.0" 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_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search for." help="(-max_charge)"/>
      <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation." help="(-intensity_threshold)"/>
      <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope)"/>
      <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th." help="(-expansion_range)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output consensusXML file were the pairs of the feature are written into." 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 pair ratios on enhanced resolution (zoom) scans.


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

@REFERENCES@
</help>
</tool>