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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>ConsensusID</name>
    
    <shortDescription>
        Computes a consensus identification from peptide identifications of several identification engines.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Computes a consensus identification from peptide identifications of several identification engines.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html">Web Documentation for ConsensusID</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="rt_delta">Maximum allowed precursor RT deviation between identifications.</option>
		<option name="mz_delta">Maximum allowed precursor m/z deviation between identifications.</option>
		<option name="min_length">Minimum of length of peptides for final consensus list</option>
		<option name="use_all_hits">If 'true' not only the first hit, but all are used (peptides only)</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="algorithm">Algorithm used for the consensus scoring.#br#ranked -- reorders the hits according to a consensus score computed from the ranks in the input runs. The score is normalized to the interval (0,100). The PeptideIdentifications do not need to have the same score type.#br#average -- reorders the hits according to the average score of the input runs. Make sure to use PeptideIdentifications with the same score type only!#br#PEPMatrix -- calculates a consensus score based on posterior error probabilities and scoring matrices for siimilarity. This algorithm uses the PAM30MS matrix to score sequences not listed by all engines. Make sure to use PeptideIdentifications with score types converted to PEPs only!#br#PEPIons -- calculates a consensus score based on posterior error probabilities and fragment ion siimilarity. Make sure to use PeptideIdentifications with score types converted to PEPs only!#br#Minimum -- calculates a consensus score based on the minimal score. Make sure to use PeptideIdentifications with score types converted to PEPs only!#br#</option>
		<option name="considered_hits">The number of top hits that are used for the consensus scoring.</option>
		<option name="number_of_runs">The number of runs used as input. This information is used in 'Ranked' and 'Average' to compute the new scores. If not given, the number of input identifications is taken.</option>
		<option name="MinNumberOfFragments">The minimal number of similar (between two suggested sequences) fragment ion masses that is necessary to evaluate the shared peak count similarity (SPC).</option>
		<option name="common">Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -&gt; pep 1 with score x1 and engine2 -&gt; pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 &gt;= common, Note that 0 &lt;= degree of similarity &lt;= 1. Values &gt; 1 will disable this option.</option>
		<option name="common">Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -&gt; pep 1 with score x1 and engine2 -&gt; pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 &gt;= common, Note that 0 &lt;= degree of similarity &lt;= 1. Values &gt; 1 will disable this option.</option>
		<option name="penalty">Give the gap penalty (the same penalty will be used for opening and extension) as a positive integer</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [idXML,featureXML,consensusXML]">input file [idXML,featureXML,consensusXML]</inPort>
		<outPort index="0" name="out [idXML,featureXML,consensusXML]">output file [idXML,featureXML,consensusXML]</outPort>
 </ports>
    <views>
        <view index="0" name="ConsensusID Std Output">The text sent to standard out during the execution of ConsensusID.</view>
        <view index="1" name="ConsensusID Error Output">The text sent to standard error during the execution of ConsensusID. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
