<?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>HighResPrecursorMassCorrector</name>
    
    <shortDescription>
        Corrects the precursor mass and charge determined by the instrument software.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Corrects the precursor mass and charge determined by the instrument software.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html">Web Documentation for HighResPrecursorMassCorrector</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="mz_tolerance">The precursor mass tolerance. Used to determine matching to feature mass traces.</option>
		<option name="mz_tolerance_unit">Unit of precursor mass tolerance</option>
		<option name="rt_tolerance">Additional retention time tolerance added to feature boundaries.</option>
		<option name="max_trace">Maximum isotopic trace considered in matching a precursor to a feature.</option>
		<option name="believe_charge">Assume precursor charge to be correct.</option>
		<option name="keep_original">Make a copy of the precursor and MS2 (true) or discard the original (false).</option>
		<option name="assign_all_matching">Correct a precursor using all matching features (true) or only the nearest (false). Only evaluated if copies are created (feature:keep_original).</option>
		<option name="mz_tolerance">The precursor mass tolerance to find the closest MS1 peak. Set to 0.0 to disable.</option>
		<option name="mz_tolerance_unit">Unit of precursor mass tolerance</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Input file (centroided data) [mzML]</inPort>
		<inPort index="1" name="in [featureXML]">Features used to correct precursor masses. [featureXML,opt.]</inPort>
		<outPort index="0" name="out [mzML]">Output file [mzML]</outPort>
		<outPort index="1" name="out_csv [csv,Inactive]">Optional CSV output file for results on 'nearest_peak' algorithm (see corresponding subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ. [csv,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="HighResPrecursorMassCorrector Std Output">The text sent to standard out during the execution of HighResPrecursorMassCorrector.</view>
        <view index="1" name="HighResPrecursorMassCorrector Error Output">The text sent to standard error during the execution of HighResPrecursorMassCorrector. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
