<?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>FeatureLinkerUnlabeled</name>
    
    <shortDescription>
        Groups corresponding features from multiple maps.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Groups corresponding features from multiple maps.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html">Web Documentation for FeatureLinkerUnlabeled</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="keep_subelements">For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.</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="second_nearest_gap">Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.</option>
		<option name="use_identifications">Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).</option>
		<option name="ignore_charge">false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state</option>
		<option name="max_difference">Never pair features with a larger RT distance (in seconds).</option>
		<option name="exponent">Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)</option>
		<option name="weight">Final RT distances are weighted by this factor</option>
		<option name="max_difference">Never pair features with larger m/z distance (unit defined by 'unit')</option>
		<option name="unit">Unit of the 'max_difference' parameter</option>
		<option name="exponent">Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)</option>
		<option name="weight">Final m/z distances are weighted by this factor</option>
		<option name="exponent">Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)</option>
		<option name="weight">Final intensity distances are weighted by this factor</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [featureXML,consensusXML]">input files separated by blanks [featureXML,consensusXML]</inPort>
		<outPort index="0" name="out [consensusXML]">Output file [consensusXML]</outPort>
 </ports>
    <views>
        <view index="0" name="FeatureLinkerUnlabeled Std Output">The text sent to standard out during the execution of FeatureLinkerUnlabeled.</view>
        <view index="1" name="FeatureLinkerUnlabeled Error Output">The text sent to standard error during the execution of FeatureLinkerUnlabeled. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
