view ConsensusMapNormalizer.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?xml version="1.0" encoding="UTF-8"?>
  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
  <!--Proposed Tool Section: [Map Alignment]-->
  <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="references"/>
    <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 $param_algorithm_type:
  -algorithm_type
  #if &quot; &quot; in str($param_algorithm_type):
    &quot;$param_algorithm_type&quot;
  #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 format="consensusxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-algorithm_type) " label="The normalization algorithm that is applied" name="param_algorithm_type" optional="True" type="select" value="robust_regression">
        <option value="robust_regression">robust_regression</option>
        <option value="median">median</option>
        <option value="quantile">quantile</option>
      </param>
      <param help="(-ratio_threshold) " 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" max="1.0" min="0.001" name="param_ratio_threshold" optional="True" type="float" value="0.67"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="consensusxml" name="param_out"/>
    </outputs>
    <help>Normalizes maps of one consensusXML file


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