<?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="PeakPickerHiRes" description="Finds mass spectrometric peaks in profile mass spectra.">
    <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;PeakPickerHiRes&apos;">
      <ITEM name="in" value="" type="input-file" description="input profile data file " required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="out" value="" type="output-file" description="output peak file " required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="processOption" value="inmemory" type="string" description="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" required="false" advanced="true" restrictions="inmemory,lowmemory" />
      <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">
        <ITEM name="signal_to_noise" value="0" type="double" description="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" required="false" advanced="false" restrictions="0:" />
        <ITEM name="spacing_difference_gap" value="4" type="double" description="The extension of a peak is stopped if the spacing between two subsequent data points exceeds &apos;spacing_difference_gap * min_spacing&apos;. &apos;min_spacing&apos; is the smaller of the two spacings from the peak apex to its two neighboring points. &apos;0&apos; to disable the constraint. Not applicable to chromatograms." required="false" advanced="true" restrictions="0:" />
        <ITEM name="spacing_difference" value="1.5" type="double" description="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter &apos;missing&apos;). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. &apos;0&apos; to disable the constraint. Not applicable to chromatograms." required="false" advanced="true" restrictions="0:" />
        <ITEM name="missing" value="1" type="int" description="Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds &apos;spacing_difference * min_spacing&apos;. &apos;min_spacing&apos; is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms." required="false" advanced="true" restrictions="0:" />
        <ITEMLIST name="ms_levels" type="int" description="List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren&apos;t picked yet will get picked. Other scans are copied to the output without changes." required="false" advanced="false" restrictions="1:">
        </ITEMLIST>
        <ITEM name="report_FWHM" value="false" type="string" description="Add metadata for FWHM (as floatDataArray named &apos;FWHM&apos; or &apos;FWHM_ppm&apos;, depending on param &apos;report_FWHM_unit&apos;) for each picked peak." required="false" advanced="false" restrictions="true,false" />
        <ITEM name="report_FWHM_unit" value="relative" type="string" description="Unit of FWHM. Either absolute in the unit of input, e.g. &apos;m/z&apos; for spectra, or relative as ppm (only sensible for spectra, not chromatograms)." required="false" advanced="false" restrictions="relative,absolute" />
        <NODE name="SignalToNoise" description="">
          <ITEM name="max_intensity" value="-1" type="int" description="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change &apos;auto_mode&apos; to &apos;-1&apos;)! All intensities EQUAL/ABOVE &apos;max_intensity&apos; will be added to the LAST histogram bin. If you choose &apos;max_intensity&apos; too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing &apos;bin_count&apos;, which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." required="false" advanced="true" restrictions="-1:" />
          <ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for &apos;max_intensity&apos; estimation (if &apos;auto_mode&apos; == 0): mean + &apos;auto_max_stdev_factor&apos; * stdev" required="false" advanced="true" restrictions="0:999" />
          <ITEM name="auto_max_percentile" value="95" type="int" description="parameter for &apos;max_intensity&apos; estimation (if &apos;auto_mode&apos; == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" />
          <ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --&gt; use &apos;max_intensity&apos;; 0 --&gt; &apos;auto_max_stdev_factor&apos; method (default); 1 --&gt; &apos;auto_max_percentile&apos; method" required="false" advanced="true" restrictions="-1:1" />
          <ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="false" restrictions="1:" />
          <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="false" restrictions="3:" />
          <ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="false" restrictions="1:" />
          <ITEM name="noise_for_empty_window" value="1e+20" type="double" description="noise value used for sparse windows" required="false" advanced="true" />
          <ITEM name="write_log_messages" value="true" type="string" description="Write out log messages in case of sparse windows or median in rightmost histogram bin" required="false" advanced="false" restrictions="true,false" />
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
