<?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: [File Handling]-->
  <tool id="IDMerger" name="IDMerger" version="2.0.0">
    <description>Merges several protein/peptide identification files into one file.</description>
    <macros>
      <token name="@EXECUTABLE@">IDMerger</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>IDMerger

-in
$param_in1
#for $infile in $inputs
    $infile.param_in
#end for
  -out $param_out
#if $param_add_to:
  -add_to $param_add_to
#end if
#if $param_annotate_file_origin:
  -annotate_file_origin
#end if
#if $param_pepxml_protxml:
  -pepxml_protxml
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
<param name="param_in1" type="data" format="idxml" label="Input files" help="(-in)" /> 
    <repeat name="inputs" title="Input files">
	<param name="param_in" type="data" format="idxml" label="Input files" help="(-in)" />
    </repeat>

      <param format="xml" help="(-add_to) 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)" label="Optional input file" name="param_add_to" optional="True" type="data"/>
      <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each protein/peptide identification (meta value: file_origin)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
      <param checked="false" falsevalue="" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'" label="Merge idXML files derived from a pepXML and corresponding protXML file" name="param_pepxml_protxml" optional="True" truevalue="-pepxml_protxml" type="boolean"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>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</help>
  </tool>