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<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="generic_node.png" type="Manipulator">
    <name>ProteinInference</name>
    
    <shortDescription>
        Protein inference based on the number of identified peptides.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Protein inference based on the number of identified peptides.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html">Web Documentation for ProteinInference</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="min_peptides_per_protein">Minimal number of peptides needed for a protein identification</option>
		<option name="treat_charge_variants_separately">If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences.</option>
		<option name="treat_modification_variants_separately">If this flag is set, different modification variants of the same peptide sequence count as individual evidences.</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 file [idXML]</inPort>
		<outPort index="0" name="out [idXML]">output file [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="ProteinInference Std Output">The text sent to standard out during the execution of ProteinInference.</view>
        <view index="1" name="ProteinInference Error Output">The text sent to standard error during the execution of ProteinInference. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
