<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="generic_node.png" type="Manipulator">
    <name>IDMerger</name>
    
    <shortDescription>
        Merges several protein/peptide identification files into one file.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Merges several protein/peptide identification files into one file.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html">Web Documentation for IDMerger</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="annotate_file_origin">Store the original filename in each protein/peptide identification (meta value: file_origin).</option>
		<option name="pepxml_protxml">Merge idXML files derived from a pepXML and corresponding protXML file.
Exactly two input files are expected in this case. Not compatible with 'add_to'.</option>
		<option name="log">Name of log file (created only when specified)</option>
		<option name="debug">Sets the debug level</option>
		<option name="threads">Sets the number of threads allowed to be used by the TOPP tool</option>
		<option name="no_progress">Disables progress logging to command line</option>
		<option name="force">Overwrite tool specific checks.</option>
		<option name="test">Enables the test mode (needed for internal use only)</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [idXML]">Input files separated by blanks [idXML]</inPort>
		<inPort index="1" name="add_to [idXML]">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). [idXML,opt.]</inPort>
		<outPort index="0" name="out [idXML]">Output file [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="IDMerger Std Output">The text sent to standard out during the execution of IDMerger.</view>
        <view index="1" name="IDMerger Error Output">The text sent to standard error during the execution of IDMerger. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
