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    <name>FeatureFinderCentroided</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_FeatureFinderCentroided.html">Web Documentation for FeatureFinderCentroided</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="debug">When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).</option>
		<option name="bins">Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map.</option>
		<option name="mz_tolerance">Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!</option>
		<option name="min_spectra">Number of spectra that have to show a similar peak mass in a mass trace.</option>
		<option name="max_missing">Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!</option>
		<option name="slope_bound">The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot.</option>
		<option name="charge_low">Lowest charge to search for.</option>
		<option name="charge_high">Highest charge to search for.</option>
		<option name="mz_tolerance">Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!</option>
		<option name="intensity_percentage">Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.</option>
		<option name="intensity_percentage_optional">Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.</option>
		<option name="optional_fit_improvement">Minimal percental improvement of isotope fit to allow leaving out an optional peak.</option>
		<option name="mass_window_width">Window width in Dalton for precalculation of estimated isotope distributions.</option>
		<option name="abundance_12C">Rel. abundance of the light carbon. Modify if labeled.</option>
		<option name="abundance_14N">Rel. abundance of the light nitrogen. Modify if labeled.</option>
		<option name="min_score">Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.</option>
		<option name="max_iterations">Maximum number of iterations of the fit.</option>
		<option name="min_score">Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.</option>
		<option name="min_isotope_fit">Minimum isotope fit of the feature before model fitting.</option>
		<option name="min_trace_score">Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension.</option>
		<option name="min_rt_span">Minimum RT span in relation to extended area that has to remain after model fitting.</option>
		<option name="max_rt_span">Maximum RT span in relation to extended area that the model is allowed to have.</option>
		<option name="rt_shape">Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.</option>
		<option name="max_intersection">Maximum allowed intersection of features.</option>
		<option name="reported_mz">The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.</option>
		<option name="rt_tolerance">Allowed RT deviation of seeds from the user-specified seed position.</option>
		<option name="mz_tolerance">Allowed m/z deviation of seeds from the user-specified seed position.</option>
		<option name="min_score">Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.</option>
		<option name="pseudo_rt_shift">Pseudo RT shift used when .</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">input file [mzML]</inPort>
		<inPort index="1" name="seeds [featureXML]">User specified seed list [featureXML,opt.]</inPort>
		<outPort index="0" name="out [featureXML]">output file [featureXML]</outPort>
		<outPort index="1" name="out_mzq [mzq]">Optional output file of MzQuantML. [mzq]</outPort>
 </ports>
    <views>
        <view index="0" name="FeatureFinderCentroided Std Output">The text sent to standard out during the execution of FeatureFinderCentroided.</view>
        <view index="1" name="FeatureFinderCentroided Error Output">The text sent to standard error during the execution of FeatureFinderCentroided. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
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