comparison ConsensusMapNormalizer.xml @ 0:3070d71e0e5c draft

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0:3070d71e0e5c

<?xml version='1.0' encoding='UTF-8'?>
<tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.0.0">
  <description>Normalizes maps of one consensusXML file</description>
  <macros>
    <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ConsensusMapNormalizer

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_type:
  -algorithm_type
  #if " " in str($param_algorithm_type):
    "$param_algorithm_type"
  #else
    $param_algorithm_type
  #end if
#end if
#if $param_ratio_threshold:
  -ratio_threshold $param_ratio_threshold
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="consensusxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_algorithm_type" type="select" optional="True" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) ">
      <option value="robust_regression">robust_regression</option>
      <option value="median">median</option>
      <option value="quantile">quantile</option>
    </param>
    <param name="param_ratio_threshold" type="float" min="0.001" max="1.0" optional="True" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" help="(-ratio_threshold) "/>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
  </outputs>
  <help>**What it does**

Normalizes maps of one consensusXML file


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html</help>
  <expand macro="references"/>
</tool>