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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>MultiplexResolver</name>
    
    <shortDescription>
        Completes peptide multiplets and resolves conflicts within them.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Completes peptide multiplets and resolves conflicts within them.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MultiplexResolver.html">Web Documentation for MultiplexResolver</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</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>
		<option name="labels">Labels used for labelling the samples. [...] specifies the labels for a single sample. For example

[][Lys8,Arg10]        ... SILAC
[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC
[Dimethyl0][Dimethyl6]        ... Dimethyl
[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl
[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL</option>
		<option name="missed_cleavages">Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)</option>
		<option name="mass_tolerance">Mass tolerance in Da for matching the detected to the theoretical mass shifts.</option>
		<option name="Arg6">Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188</option>
		<option name="Arg10">Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267</option>
		<option name="Lys4">Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481</option>
		<option name="Lys6">Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188</option>
		<option name="Lys8">Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259</option>
		<option name="Leu3">Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262</option>
		<option name="Dimethyl0">Dimethyl  |  H(4) C(2)  |  unimod #36</option>
		<option name="Dimethyl4">Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199</option>
		<option name="Dimethyl6">Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510</option>
		<option name="Dimethyl8">Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330</option>
		<option name="ICPL0">ICPL  |  H(3) C(6) N O  |  unimod #365</option>
		<option name="ICPL4">ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687</option>
		<option name="ICPL6">ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364</option>
		<option name="ICPL10">ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [consensusXML]">Peptide multiplets with assigned sequence information [consensusXML]</inPort>
		<outPort index="0" name="out [consensusXML]">Complete peptide multiplets. [consensusXML]</outPort>
		<outPort index="1" name="out_conflicts [consensusXML,Inactive]">Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information. [consensusXML,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="MultiplexResolver Std Output">The text sent to standard out during the execution of MultiplexResolver.</view>
        <view index="1" name="MultiplexResolver Error Output">The text sent to standard error during the execution of MultiplexResolver. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
