view FeatureLinkerLabeled.xml @ 1:17e8c91b70d5 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="1.12.0">
  <description>Groups corresponding isotope-labeled features in a feature map.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureLinkerLabeled

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
${param_rt_estimate}
-algorithm:rt_pair_dist ${param_rt_pair_dist}
-algorithm:rt_dev_low ${param_rt_dev_low}
-algorithm:rt_dev_high ${param_rt_dev_high}
-algorithm:mz_pair_dists ${param_mz_pair_dists}
-algorithm:mz_dev ${param_mz_dev}
#if $adv_opts.adv_opts_selector=='advanced':
    ${adv_opts.param_mrm}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" label="Input file" help="(-in)"/>
    <param name="param_rt_estimate" type="boolean" truevalue="-algorithm:rt_estimate true" falsevalue="-algorithm:rt_estimate false" checked="true" optional="True" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance." help="(-rt_estimate)"/>
    <param name="param_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist)"/>
    <param name="param_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low)"/>
    <param name="param_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high)"/>
    <param name="param_mz_pair_dists" type="text" size="20" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)" help="(-mz_pair_dists)"/>
    <param name="param_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance#br#" help="(-mz_dev)"/>
    <expand macro="advanced_options">
      <param name="param_mrm" type="boolean" truevalue="-algorithm:mrm true" falsevalue="-algorithm:mrm false" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file" format="consensusXML"/>
  </outputs>
  <help>**What it does**

Groups corresponding isotope-labeled features in a feature map.


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

@REFERENCES@
</help>
</tool>