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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>IDMapper</name>
    
    <shortDescription>
        Assigns protein/peptide identifications to features or consensus features.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Assigns protein/peptide identifications to features or consensus features.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html">Web Documentation for IDMapper</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="rt_tolerance">RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.
Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.</option>
		<option name="mz_tolerance">m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.
Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.</option>
		<option name="mz_measure">Unit of 'mz_tolerance'.</option>
		<option name="mz_reference">Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',
masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.
('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)</option>
		<option name="ignore_charge">For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.</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="use_centroid_rt">Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces.</option>
		<option name="use_centroid_mz">Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.
(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)</option>
		<option name="use_subelements">Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.</option>
		<option name="annotate_ids_with_subelements">Store the map index of the sub-feature in the peptide ID.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="id [mzid,idXML]">Protein/peptide identifications file [mzid,idXML]</inPort>
		<inPort index="1" name="in [featureXML,consensusXML,mzq]">Feature map/consensus map file [featureXML,consensusXML,mzq]</inPort>
		<outPort index="0" name="out [featureXML,consensusXML,mzq]">Output file (the format depends on the input file format). [featureXML,consensusXML,mzq]</outPort>
 </ports>
    <views>
        <view index="0" name="IDMapper Std Output">The text sent to standard out during the execution of IDMapper.</view>
        <view index="1" name="IDMapper Error Output">The text sent to standard error during the execution of IDMapper. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
