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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.#br#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.#br#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',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('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.#br#(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>
