<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_2.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="" type="string" description="input file (valid formats: 'mzData')" />
      <ITEM name="out" value="" type="string" description="output feature list (valid formats: 'featureXML')" />
      <ITEM name="type" value="centroided" type="string" description="FeatureFinder algorithm type#br#" restrictions="isotope_wavelet,centroided,simple,simplest,wavelet" />
      <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" restrictions="true,false" />
      <NODE name="algorithm" description="Algorithm section">
        <ITEM name="debug" value="0" type="int" description="If not 0 debug mode is activated. Then several files with intermediate results are written." restrictions="0-1" />
        <NODE name="intensity" description="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)">
          <ITEM name="bins" value="10" type="int" description="Number of bins per dimension (RT and m/z)." restrictions="1-" />
        </NODE>
        <NODE name="mass_trace" description="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">
          <ITEM name="mz_tolerance" value="0.06" type="float" description="m/z difference tolerance of peaks belonging to the same mass trace." restrictions="0-" />
          <ITEM name="min_spectra" value="14" type="int" description="Number of spectra the have to show the same peak mass for a mass trace." restrictions="1-" />
          <ITEM name="max_missing" value="4" type="int" description="Number of spectra where a high mass deviation or missing peak is acceptable." restrictions="0-" />
          <ITEM name="slope_bound" value="0.1" type="float" description="The maximum slope of mass trace intensities when extending from the highest peak"  restrictions="0-" />
        </NODE>
        <NODE name="isotopic_pattern" description="Settings for the calculation of a score indicating if a peak is part of a isotoipic pattern (between 0 and 1).">
          <ITEM name="charge_low" value="1" type="int" description="Lowest charge to search for." restrictions="1-" />
          <ITEM name="charge_high" value="4" type="int" description="Highest charge to search for." restrictions="1-" />
          <ITEM name="mz_tolerance" value="0.06" type="float" description="Tolerated mass deviation from the theoretical isotopic pattern." restrictions="0-" />
          <ITEM name="intensity_percentage" value="10" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present."  restrictions="0-100" />
          <ITEM name="intensity_percentage_optional" value="0.1" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing."  restrictions="0-100" />
          <ITEM name="optional_fit_improvement" value="2" type="float" description="Minimal percental improvement of isotope fit to allow leaving out an optional peak."  restrictions="0-100" />
          <ITEM name="mass_window_width" value="100" type="float" description="Window width in Dalton for precalcuation of estimated isotope distribtions."  restrictions="1-200" />
        </NODE>
        <NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)">
          <ITEM name="min_feature_score" value="0.7" type="float" description="Overall score threshold for a feature to be reported." restrictions="0-1" />
          <ITEM name="min_seed_score" value="0.8" type="float" description="Minimum score a peak has to have to be used as seed.#br#The score is calculated as the geometric mean of intensity, mass trace score and isotope pattern score." restrictions="0-1" />
          <ITEM name="min_isotope_fit" value="0.8" type="float" description="Minimum isotope fit quality."  restrictions="0-1" />
          <ITEM name="min_trace_score" value="0.5" type="float" description="Trace score threshold.#br#Traces below this threshold are removed after the fit."  restrictions="0-1" />
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
