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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="FeatureFinder" description="">
<NODE name="1" description="Instance '1' section for 'FeatureFinder'">
<ITEM name="in" value="example.dta2d" type="string" />
<ITEM name="out" value="features.xml" type="string"/>
<ITEM name="type" value="simplest" type="string" description="FeatureFinder algorithm type ('simple', )" />
<ITEM name="log" value="TOPP.log" type="string" description="Location of the log file" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" />
<NODE name="algorithm" description="Algorithm section">
<NODE name="seeder" description="Settings for the seeder (Determines potential feature regions)">
<ITEM name="min_intensity" value="16000" type="float" description="Absolute value for the minimum intensity of a seed. If set to 0, a fixed percentage of the intensity of the largest peak is taken (see intensity_perc)." />
<ITEM name="signal_to_noise" value="0.0" type="float" description="SignalToNoise (S/N) ratio." restrictions="0:" />
</NODE>
<NODE name="extender" description="Settings for the extender (Collects all peaks belonging to a feature)">
<ITEM name="dist_mz_up" value="5.0" type="float" description="maximum high m/z distance of peak in the region/boundary from the seed" />
<ITEM name="dist_mz_down" value="3.0" type="float" description="maximum low m/z distance of peak in the region/boundary from the seed" />
<ITEM name="dist_rt_up" value="10.0" type="float" description="maximum high RT distance of peak in the region/boundary from the seed" />
<ITEM name="dist_rt_down" value="10.0" type="float" description="maximum low RT distance of peak in the region/boundary from the seed" />
<ITEM name="priority_thr" value="-0.1" type="float" description="Minimum priority for data points to be included into the boundary of the feature (default 0.0)The priority of a data point is a function of its intensity and its distance to the last pointincluded into the feature region. Setting this threshold to zero or a very small value isusually a good idea." />
<ITEM name="intensity_factor" value="0.01" type="float" description="Influences for intensity (ion count) threshold in the feature extension. We include only raw datapoints into this region if their intensity is larger than [intensity_factor * (intensity of the seed)]." />
</NODE>
<NODE name="fitter" description="Settings for the modefitter (Fits a model to the data determinging the probapility that they represent a feature.)">
<ITEM name="tolerance_stdev_bounding_box" value="3" type="float" description="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" />
<ITEM name="intensity_cutoff_factor" value="0.03" type="float" description="Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model" />
<ITEM name="feature_intensity_sum" value="1" type="int" description="Determines what is reported as feature intensity.#br#1: the sum of peak intensities;#br#0: the maximum intensity of all peaks" />
<NODE name="min_num_peaks" description="Required number of peaks for a feature.">
<ITEM name="final" value="5" type="int" description="Minimum number of peaks left after cutoff. If smaller, feature will be discarded." />
<ITEM name="extended" value="10" type="int" description="Minimum number of peaks after extension. If smaller, feature will be discarded." />
</NODE>
<NODE name="mz" description="Model settings in m/z dimension.">
<ITEM name="interpolation_step" value="0.03" type="float" description="Interpolation step size for m/z." />
<NODE name="model_type" description="">
<ITEM name="first" value="1" type="int" description="Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian)." />
<ITEM name="last" value="2" type="int" description="Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian)." />
</NODE>
</NODE>
<NODE name="quality" description="Fitting quality settings.">
<ITEM name="type" value="Correlation" type="string" description="Type of the quality measure used to assess the fit of model vs data ('Correlation','EuclidianDistance','RankCorrelation')." />
<ITEM name="minimum" value="0.65" type="float" description="Minimum quality of fit, features below this threshold are discarded." />
</NODE>
<NODE name="isotope_model" description="Settings of the isotope model (m/z).">
<NODE name="stdev" description="Instrument resolution settings for m/z dimension.">
<ITEM name="first" value="0.16" type="float" description="First standard deviation to be considered for isotope model." />
<ITEM name="last" value="0.16" type="float" description="Last standard deviation to be considered for isotope model." />
<ITEM name="step" value="0.04" type="float" description="Step size for standard deviations considered for isotope model." />
</NODE>
<NODE name="averagines" description="Averagines are used to approximate the number of atoms (C,H,N,O,S) which a peptide of a given mass contains.">
<ITEM name="C" value="0.0443" type="float" description="Number of C atoms per Dalton of the mass." />
<ITEM name="H" value="0.007" type="float" description="Number of H atoms per Dalton of the mass." />
<ITEM name="N" value="0.0012" type="float" description="Number of N atoms per Dalton of the mass." />
<ITEM name="O" value="0.013" type="float" description="Number of O atoms per Dalton of the mass." />
<ITEM name="S" value="0.00037" type="float" description="Number of S atoms per Dalton of the mass." />
</NODE>
<NODE name="isotope" description="">
<ITEM name="trim_right_cutoff" value="0.001" type="float" description="Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered." />
<ITEM name="maximum" value="4" type="int" description="Maximum number of isotopes being used for the IsotopeModel." />
<ITEM name="distance" value="1.000495" type="float" description="Distance between consecutive isotopic peaks." />
</NODE>
</NODE>
</NODE>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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