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    <name>FeatureFinderMetabo</name>
    
    <shortDescription>
        Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html">Web Documentation for FeatureFinderMetabo</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="noise_threshold_int">Intensity threshold below which peaks are regarded as noise.</option>
		<option name="chrom_peak_snr">Minimum signal-to-noise a mass trace should have.</option>
		<option name="chrom_fwhm">Expected chromatographic peak width (in seconds).</option>
		<option name="mass_error_ppm">Allowed mass deviation (in ppm).</option>
		<option name="reestimate_mt_sd">Enables dynamic re-estimation of m/z variance during mass trace collection stage.</option>
		<option name="quant_method">Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data.</option>
		<option name="trace_termination_criterion">Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold.</option>
		<option name="trace_termination_outliers">Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.</option>
		<option name="min_sample_rate">Minimum fraction of scans along the mass trace that must contain a peak.</option>
		<option name="min_trace_length">Minimum expected length of a mass trace (in seconds).</option>
		<option name="max_trace_length">Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.</option>
		<option name="enabled">Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection.</option>
		<option name="width_filtering">Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.</option>
		<option name="min_fwhm">Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.</option>
		<option name="max_fwhm">Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.</option>
		<option name="masstrace_snr_filtering">Apply post-filtering by signal-to-noise ratio after smoothing.</option>
		<option name="local_rt_range">RT range where to look for coeluting mass traces</option>
		<option name="local_mz_range">MZ range where to look for isotopic mass traces</option>
		<option name="charge_lower_bound">Lowest charge state to consider</option>
		<option name="charge_upper_bound">Highest charge state to consider</option>
		<option name="report_summed_ints">Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.</option>
		<option name="enable_RT_filtering">Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..</option>
		<option name="isotope_filtering_model">Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.</option>
		<option name="mz_scoring_13C">Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.).</option>
		<option name="use_smoothed_intensities">Use LOWESS intensities instead of raw intensities.</option>
		<option name="report_convex_hulls">Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Centroided mzML file [mzML]</inPort>
		<outPort index="0" name="out [featureXML]">FeatureXML file with metabolite features [featureXML]</outPort>
 </ports>
    <views>
        <view index="0" name="FeatureFinderMetabo Std Output">The text sent to standard out during the execution of FeatureFinderMetabo.</view>
        <view index="1" name="FeatureFinderMetabo Error Output">The text sent to standard error during the execution of FeatureFinderMetabo. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
