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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="1.12.0">
  <description>Groups corresponding features from multiple maps.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureLinkerUnlabeled

-in ${param_in}
-out ${param_out}
${param_keep_subelements}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:second_nearest_gap ${param_second_nearest_gap}
${param_use_identifications}
${param_ignore_charge}
-algorithm:distance_RT:max_difference ${param_max_difference}
-algorithm:distance_MZ:max_difference ${param_max_difference}
-algorithm:distance_MZ:unit ${param_unit}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
    -algorithm:distance_RT:weight ${adv_opts.param_weight}
    -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
    -algorithm:distance_MZ:weight ${adv_opts.param_weight}
    -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
    -algorithm:distance_intensity:weight ${adv_opts.param_weight}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
    <param name="param_keep_subelements" type="boolean" truevalue="-keep_subelements true" falsevalue="-keep_subelements false" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." help="(-keep_subelements)"/>
    <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/>
    <param name="param_use_identifications" type="boolean" truevalue="-algorithm:use_identifications true" falsevalue="-algorithm:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/>
    <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge true" falsevalue="-algorithm:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/>
    <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/>
    <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/>
    <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)">
      <option value="Da">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/>
      <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/>
      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
      <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file" format="consensusXML"/>
  </outputs>
  <help>**What it does**

Groups corresponding features from multiple maps.


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

@REFERENCES@
</help>
</tool>