view IDMerger.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="IDMerger" name="IDMerger" version="1.12.0">
  <description>Merges several protein/peptide identification files into one file.</description>
  <macros>
    <token name="@EXECUTABLE@">IDMerger</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDMerger

-in ${param_in}
-out ${param_out}
-add_to ${param_add_to}
${param_annotate_file_origin}
${param_pepxml_protxml}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="idXML" optional="False" size="20" label="Input files separated by blanks" help="(-in)"/>
    <param name="param_add_to" type="data" format="idXML" optional="True" label="Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)." help="(-add_to)"/>
    <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)." help="(-annotate_file_origin)"/>
    <param name="param_pepxml_protxml" type="boolean" truevalue="-pepxml_protxml true" falsevalue="-pepxml_protxml false" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." help="(-pepxml_protxml)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file" format="idXML"/>
  </outputs>
  <help>**What it does**

Merges several protein/peptide identification files into one file.


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

@REFERENCES@
</help>
</tool>