view MapRTTransformer.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MapRTTransformer" name="MapRTTransformer" version="1.12.0">
  <description>Applies retention time transformations to maps.</description>
  <macros>
    <token name="@EXECUTABLE@">MapRTTransformer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MapRTTransformer

-in ${param_in}
-out ${param_out}
-trafo_in ${param_trafo_in}
-trafo_out ${param_trafo_out}
${param_invert}
-threads \${GALAXY_SLOTS:-24} 
-model:type ${param_type}
${param_symmetric_regression}
-model:interpolated:interpolation_type ${param_interpolation_type}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML,featureXML,consensusXML,idXML" optional="True" size="20" label="Input files to transform (separated by blanks)" help="(-in)"/>
    <param name="param_trafo_in" type="data" format="" optional="False" size="20" label="Transformations to apply (files separated by blanks)" help="(-trafo_in)"/>
    <param name="param_invert" type="boolean" truevalue="-invert true" falsevalue="-invert false" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert)"/>
    <param name="param_type" type="select" optional="True" value="none" label="Type of model" help="(-type)">
      <option value="none">none</option>
      <option value="linear">linear</option>
      <option value="b_spline">b_spline</option>
      <option value="interpolated">interpolated</option>
    </param>
    <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
    <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)">
      <option value="linear">linear</option>
      <option value="cspline">cspline</option>
      <option value="akima">akima</option>
    </param>
  </inputs>
  <outputs>
    <data name="param_out" label="Output files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together." format="idXML">
      <change_format>
        <when input="param_out_type" value="mzML" format="mzML"/>
        <when input="param_out_type" value="featureXML" format="featureXML"/>
        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
      </change_format>
    </data>
    <data name="param_trafo_out" label="Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together." format="data"/>
  </outputs>
  <help>**What it does**

Applies retention time transformations to maps.


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

@REFERENCES@
</help>
</tool>