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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>EICExtractor</name>
    
    <shortDescription>
        Extracts intensities from dedicates positions in a LC/MS map
    </shortDescription>
    
    <fullDescription>
        <intro><p>Extracts intensities from dedicates positions in a LC/MS map</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html">Web Documentation for EICExtractor</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="rt_tol">RT tolerance in [s] for finding max peak (whole RT range around RT middle)</option>
		<option name="mz_tol">m/z tolerance in [ppm] for finding a peak</option>
		<option name="rt_collect"># of scans up &amp; down in RT from highest point for ppm estimation in result</option>
		<option name="out_separator">Separator character for output CSV 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="enabled">Automatically detect injection peaks from TIC and quantify all m/z x RT combinations.</option>
		<option name="FHWM">Expected full width at half-maximum of each raw RT peak in [s]. Gaussian smoothing filter with this width is applied to TIC.</option>
		<option name="SNThreshold">S/N threshold for a smoothed raw peak to pass peak picking. Higher thesholds will result in less peaks.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Input raw data file [mzML]</inPort>
		<inPort index="1" name="in_header [txt]">[for Waters data only] Read additional information from _HEADER.TXT. Provide one for each raw input file. [txt,opt.]</inPort>
		<inPort index="2" name="pos [edta]">Input config file stating where to find signal [edta]</inPort>
		<outPort index="0" name="out [csv]">Output quantitation file (multiple columns for each input compound) [csv]</outPort>
		<outPort index="1" name="out_debug_TIC [mzML,Inactive]">Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions [mzML,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="EICExtractor Std Output">The text sent to standard out during the execution of EICExtractor.</view>
        <view index="1" name="EICExtractor Error Output">The text sent to standard error during the execution of EICExtractor. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
