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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>Decharger</name>
    
    <shortDescription>
        Decharges and merges different feature charge variants of the same peptide.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Decharges and merges different feature charge variants of the same peptide.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.html">Web Documentation for Decharger</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</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="charge_min">Minimal possible charge</option>
		<option name="charge_max">Maximal possible charge</option>
		<option name="charge_span_max">Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge</option>
		<option name="q_try">Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').</option>
		<option name="retention_max_diff">Maximum allowed RT difference between any two features if their relation shall be determined</option>
		<option name="retention_max_diff_local">Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)</option>
		<option name="mass_max_diff">Maximum allowed mass difference [in Th] for a single feature.</option>
		<option name="potential_adducts">Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' indicate the charge, e.g. 'Ca++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file.</option>
		<option name="max_neutrals">Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!</option>
		<option name="max_minority_bound">Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant. E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct</option>
		<option name="min_rt_overlap">Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)</option>
		<option name="intensity_filter">Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge.</option>
		<option name="default_map_label">Label of map in output consensus file where all features are put by default</option>
		<option name="verbose_level">Amount of debug information given during processing.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [featureXML]">input file  [featureXML]</inPort>
		<outPort index="0" name="out_cm [consensusXML]">output consensus map [consensusXML]</outPort>
		<outPort index="1" name="out_fm [featureXML,Inactive]">output feature map [featureXML,Inactive]</outPort>
		<outPort index="2" name="outpairs [consensusXML,Inactive]">output file [consensusXML,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="Decharger Std Output">The text sent to standard out during the execution of Decharger.</view>
        <view index="1" name="Decharger Error Output">The text sent to standard error during the execution of Decharger. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
