view MRMMapper.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MRMMapper" name="MRMMapper" version="1.12.0">
  <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
  <macros>
    <token name="@EXECUTABLE@">MRMMapper</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MRMMapper

-in ${param_in}
-tr ${param_tr}
-out ${param_out}
-precursor_tolerance ${param_precursor_tolerance}
-product_tolerance ${param_product_tolerance}
${param_no-strict}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in)"/>
    <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/>
    <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance)"/>
    <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance)"/>
    <param name="param_no-strict" type="boolean" truevalue="-no-strict true" falsevalue="-no-strict false" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped." help="(-no-strict)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file containing mapped chromatograms" format="mzML"/>
  </outputs>
  <help>**What it does**

MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)


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

@REFERENCES@
</help>
</tool>