view InternalCalibration.xml @ 3:ec62782f6c68 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="InternalCalibration" name="InternalCalibration" version="1.12.0">
  <description>Applies an internal calibration.</description>
  <macros>
    <token name="@EXECUTABLE@">InternalCalibration</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>InternalCalibration

-in ${param_in}
-out ${param_out}
-ref_peaks ${param_ref_peaks}
-type ${param_type}
-trafo ${param_trafo}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:mz_tolerance ${param_mz_tolerance}
-algorithm:mz_tolerance_unit ${param_mz_tolerance_unit}
-algorithm:rt_tolerance ${param_rt_tolerance}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML,featureXML" optional="False" label="input peak file " help="(-in)"/>
    <param name="param_ref_peaks" type="data" format="tabular,idXML" optional="True" label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" help="(-ref_peaks)"/>
    <param name="param_type" type="select" optional="True" value="spectrumwise" label="The kind of internal calibration that should be applied." help="(-type)">
      <option value="spectrumwise">spectrumwise</option>
      <option value="global">global</option>
    </param>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.0" label="Allowed tolerance between peak and reference m/z." help="(-mz_tolerance)"/>
    <param name="param_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance." help="(-mz_tolerance_unit)">
      <option value="Da">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <param name="param_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt." help="(-rt_tolerance)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file " format="featureXML">
      <change_format>
        <when input="param_out_type" value="mzML" format="mzML"/>
      </change_format>
    </data>
    <data name="param_trafo" label="output transformation file (only for global calibration)" format="data"/>
  </outputs>
  <help>**What it does**

Applies an internal calibration.


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

@REFERENCES@
</help>
</tool>