<?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>ConsensusID</name>
    
    <shortDescription>
        Computes a consensus of peptide identifications of several identification engines.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Computes a consensus of 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">[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum.</option>
		<option name="mz_delta">[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum.</option>
		<option name="algorithm">Algorithm used for consensus scoring.
* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.
* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.
* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.
* worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.
* average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.
* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types.</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="considered_hits">The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits).</option>
		<option name="min_support">For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed).</option>
		<option name="count_empty">Count empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?</option>
		<option name="mass_tolerance">Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides .</option>
		<option name="min_shared">The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC).</option>
		<option name="matrix">Substitution matrix to use for alignment-based similarity scoring</option>
		<option name="penalty">Alignment gap penalty (the same value is used for gap opening and extension)</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>
