<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="PeakPickerIterative" docurl="http://www.openms.de/documentation/UTILS_PeakPickerIterative.html" category="Signal processing and preprocessing" >
<description><![CDATA[Finds mass spectrometric peaks in profile mass spectra.]]></description>
<manual><![CDATA[Finds mass spectrometric peaks in profile mass spectra.]]></manual>
<citations>
  <citation doi="10.1038/nmeth.3959" url="" />
</citations>
<PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="PeakPickerIterative" description="Finds mass spectrometric peaks in profile mass spectra.">
    <ITEM name="version" value="2.6.0-pre-exported-20201001" 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;PeakPickerIterative&apos;">
      <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="out" value="" type="output-file" description="output file" required="true" 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="bool" description="Disables progress logging to command line" required="false" advanced="true" />
      <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
      <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
      <NODE name="algorithm" description="Algorithm parameters section">
        <ITEM name="signal_to_noise_" value="1.0" type="double" description="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" required="false" advanced="false" />
        <ITEM name="peak_width" value="0.0" type="double" description="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing). In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value." required="false" advanced="false" />
        <ITEM name="spacing_difference" value="1.5" type="double" description="Difference between peaks in multiples of the minimal difference to continue. The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak." required="false" advanced="true" />
        <ITEM name="sn_bin_count_" value="30" type="int" description="Bin count for the Signal to Noise estimation." required="false" advanced="true" />
        <ITEM name="nr_iterations_" value="5" type="int" description="Nr of iterations to perform (how many times the peaks are re-centered)." required="false" advanced="true" restrictions="1:" />
        <ITEM name="sn_win_len_" value="20.0" type="double" description="Window length for the Signal to Noise estimation." required="false" advanced="true" />
        <ITEM name="check_width_internally" value="false" type="bool" description="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" required="false" advanced="true" />
        <ITEM name="ms1_only" value="false" type="bool" description="Only do MS1" required="false" advanced="false" />
        <ITEM name="clear_meta_data" value="false" type="bool" description="Delete meta data about peak width" required="false" advanced="false" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>