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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="FeatureFinderMetabo" description="Assembles metabolite features from singleton mass traces.">
<ITEM name="version" value="1.10.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'FeatureFinderMetabo'">
<ITEM name="in" value="" type="string" description="input centroided mzML file" tags="input file,required" supported_formats="*.mzML" />
<ITEM name="out" value="" type="string" description="output featureXML file with metabolite features" tags="output file,required" supported_formats="*.featureXML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="algorithm" description="Algorithm parameters section">
<NODE name="common" description="">
<ITEM name="noise_threshold_int" value="10" type="float" description="Intensity threshold below which peaks are regarded as noise." />
<ITEM name="chrom_peak_snr" value="3" type="float" description="Minimum signal-to-noise a mass trace should have." />
<ITEM name="chrom_fwhm" value="5" type="float" description="Expected chromatographic peak width (in seconds)." />
</NODE>
<NODE name="mtd" description="">
<ITEM name="mass_error_ppm" value="20" type="float" description="Allowed mass deviation (in ppm)." />
<ITEM name="reestimate_mt_sd" value="true" type="string" description="Enables dynamic re-estimation of m/z variance during mass trace collection stage." restrictions="true,false" />
<ITEM name="min_sample_rate" value="0.5" type="float" description="Minimum fraction of scans along the mass trace that must contain a peak." tags="advanced" />
<ITEM name="min_trace_length" value="5" type="float" description="Minimum expected length of a mass trace (in seconds)." tags="advanced" />
</NODE>
<NODE name="epd" description="">
<ITEM name="width_filtering" value="off" 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." restrictions="off,fixed,auto" />
<ITEM name="min_fwhm" value="3" type="float" description="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." tags="advanced" />
<ITEM name="max_fwhm" value="60" type="float" description="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." tags="advanced" />
<ITEM name="masstrace_snr_filtering" value="false" type="string" description="Apply post-filtering by signal-to-noise ratio after smoothing." tags="advanced" restrictions="false,true" />
<ITEM name="min_trace_length" value="5" type="float" description="Minimum length of a mass trace (in seconds)." tags="advanced" />
<ITEM name="max_trace_length" value="300" type="float" description="Maximum length of a mass trace (in seconds)." tags="advanced" />
</NODE>
<NODE name="ffm" description="">
<ITEM name="local_rt_range" value="10" type="float" description="RT range where to look for coeluting mass traces" tags="advanced" />
<ITEM name="local_mz_range" value="6.5" type="float" description="MZ range where to look for isotopic mass traces" tags="advanced" />
<ITEM name="charge_lower_bound" value="1" type="int" description="Lowest charge state to consider" />
<ITEM name="charge_upper_bound" value="3" type="int" description="Highest charge state to consider" />
<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." tags="advanced" restrictions="false,true" />
<ITEM name="disable_isotope_filtering" value="false" type="string" description="Disable isotope filtering." tags="advanced" restrictions="false,true" />
<ITEM name="isotope_model" value="metabolites" type="string" description="Change type of isotope model." tags="advanced" restrictions="metabolites,peptides" />
<ITEM name="use_smoothed_intensities" value="true" type="string" description="Use LOWESS intensities instead of raw intensities." tags="advanced" restrictions="false,true" />
</NODE>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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