<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="FeatureFinderMetabo" description="Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.">
    <ITEM name="version" value="2.4.0-HEAD-2018-10-30" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureFinderMetabo&apos;">
      <ITEM name="in" value="" type="input-file" description="Centroided mzML file" required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="out" value="" type="output-file" description="FeatureXML file with metabolite features" required="true" advanced="false" supported_formats="*.featureXML" />
      <ITEM name="out_chrom" value="" type="output-file" description="Optional mzML file with chromatograms" required="false" advanced="false" supported_formats="*.mzML" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="true" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
      <NODE name="algorithm" description="Algorithm parameters section">
        <NODE name="common" description="Common parameters for all other subsections">
          <ITEM name="noise_threshold_int" value="10" type="double" description="Intensity threshold below which peaks are regarded as noise." required="false" advanced="false" />
          <ITEM name="chrom_peak_snr" value="3" type="double" description="Minimum signal-to-noise a mass trace should have." required="false" advanced="false" />
          <ITEM name="chrom_fwhm" value="5" type="double" description="Expected chromatographic peak width (in seconds)." required="false" advanced="false" />
        </NODE>
        <NODE name="mtd" description="Mass Trace Detection parameters">
          <ITEM name="mass_error_ppm" value="20" type="double" description="Allowed mass deviation (in ppm)." required="false" advanced="false" />
          <ITEM name="reestimate_mt_sd" value="true" type="string" description="Enables dynamic re-estimation of m/z variance during mass trace collection stage." required="false" advanced="false" restrictions="true,false" />
          <ITEM name="quant_method" value="area" type="string" description="Method of quantification for mass traces. For LC data &apos;area&apos; is recommended, &apos;median&apos; for direct injection data." required="false" advanced="false" restrictions="area,median" />
          <ITEM name="trace_termination_criterion" value="outlier" type="string" description="Termination criterion for the extension of mass traces. In &apos;outlier&apos; mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In &apos;sample_rate&apos; mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the &apos;min_sample_rate&apos; threshold." required="false" advanced="true" restrictions="outlier,sample_rate" />
          <ITEM name="trace_termination_outliers" value="5" type="int" description="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached." required="false" advanced="true" />
          <ITEM name="min_sample_rate" value="0.5" type="double" description="Minimum fraction of scans along the mass trace that must contain a peak." required="false" advanced="true" />
          <ITEM name="min_trace_length" value="5" type="double" description="Minimum expected length of a mass trace (in seconds)." required="false" advanced="true" />
          <ITEM name="max_trace_length" value="-1" type="double" description="Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection." required="false" advanced="true" />
        </NODE>
        <NODE name="epd" description="Elution Profile Detection (to separate isobaric Mass Traces by elution time).">
          <ITEM name="enabled" value="true" type="string" description="Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection." required="false" advanced="false" restrictions="true,false" />
          <ITEM name="width_filtering" value="fixed" type="string" description="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." required="false" advanced="false" restrictions="off,fixed,auto" />
          <ITEM name="min_fwhm" value="3" type="double" description="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto." required="false" advanced="true" />
          <ITEM name="max_fwhm" value="60" type="double" description="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto." required="false" advanced="true" />
          <ITEM name="masstrace_snr_filtering" value="false" type="string" description="Apply post-filtering by signal-to-noise ratio after smoothing." required="false" advanced="true" restrictions="false,true" />
        </NODE>
        <NODE name="ffm" description="FeatureFinder parameters (assembling mass traces to charged features)">
          <ITEM name="local_rt_range" value="10" type="double" description="RT range where to look for coeluting mass traces" required="false" advanced="true" />
          <ITEM name="local_mz_range" value="6.5" type="double" description="MZ range where to look for isotopic mass traces" required="false" advanced="true" />
          <ITEM name="charge_lower_bound" value="1" type="int" description="Lowest charge state to consider" required="false" advanced="false" />
          <ITEM name="charge_upper_bound" value="3" type="int" description="Highest charge state to consider" required="false" advanced="false" />
          <ITEM name="report_summed_ints" value="false" type="string" description="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone." required="false" advanced="true" restrictions="false,true" />
          <ITEM name="enable_RT_filtering" value="true" type="string" description="Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data.." required="false" advanced="false" restrictions="false,true" />
          <ITEM name="isotope_filtering_model" value="metabolites (5% RMS)" type="string" description="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." required="false" advanced="false" restrictions="metabolites (2% RMS),metabolites (5% RMS),peptides,none" />
          <ITEM name="mz_scoring_13C" value="false" type="string" description="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.)." required="false" advanced="false" restrictions="false,true" />
          <ITEM name="use_smoothed_intensities" value="true" type="string" description="Use LOWESS intensities instead of raw intensities." required="false" advanced="true" restrictions="false,true" />
          <ITEM name="report_convex_hulls" value="true" type="string" description="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)." required="false" advanced="false" restrictions="false,true" />
          <ITEM name="remove_single_traces" value="false" type="string" description="Remove unassembled traces (single traces)." required="false" advanced="false" restrictions="false,true" />
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
