view ConsensusMapNormalizer.xml @ 8:08d69e97ad33 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

<?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="2.2.0">
  <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 $param_algorithm_type:
  -algorithm_type
  #if " " in str($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
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_accession_filter:
  -accession_filter     "$adv_opts.param_accession_filter"
#end if
    #if $adv_opts.param_description_filter:
  -description_filter     "$adv_opts.param_description_filter"
#end if
    #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" display="radio" type="select" optional="False" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
      <option value="robust_regression" selected="true">robust_regression</option>
      <option value="median">median</option>
      <option value="median_shift">median_shift</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_accession_filter" type="text" size="30" label="Use only features with accessions (partially) matching this regular expression for computing the normalization factors. Useful," help="(-accession_filter) e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_description_filter" type="text" size="30" label="Use only features with description (partially) matching this regular expression for computing the normalization factors. Useful," help="(-description_filter) e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_force" display="radio" 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>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>