<?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>FeatureFinderMRM</name>
    
    <shortDescription>
        Detects two-dimensional features in LC-MS data.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Detects two-dimensional features in LC-MS data.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html">Web Documentation for FeatureFinderMRM</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="min_rt_distance">Minimal distance of MRM features in seconds.</option>
		<option name="min_num_peaks_per_feature">Minimal number of peaks which are needed for a single feature</option>
		<option name="min_signal_to_noise_ratio">Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise.</option>
		<option name="write_debug_files">If set to true, for each feature a plot will be created, in the subdirectory 'debug'</option>
		<option name="resample_traces">If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension</option>
		<option name="write_debuginfo">If set to true, debug messages are written, the output can be somewhat lengthy.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">input file [mzML]</inPort>
		<outPort index="0" name="out [featureXML]">output file [featureXML]</outPort>
 </ports>
    <views>
        <view index="0" name="FeatureFinderMRM Std Output">The text sent to standard out during the execution of FeatureFinderMRM.</view>
        <view index="1" name="FeatureFinderMRM Error Output">The text sent to standard error during the execution of FeatureFinderMRM. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
