<?xml version="1.0" encoding="UTF-8"?>
<tool version="2.0.0" name="OpenSwathChromatogramExtractor" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html" category="Targeted Experiments" >
<description><![CDATA[Extract chromatograms (XIC) from a MS2 map file.]]></description>
<manual><![CDATA[Extract chromatograms (XIC) from a MS2 map file.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="OpenSwathChromatogramExtractor" description="Extract chromatograms (XIC) from a MS2 map file.">
    <ITEM name="version" value="2.0.0" 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;OpenSwathChromatogramExtractor&apos;">
      <ITEMLIST name="in" type="input-file" description="Input files separated by blank" required="true" advanced="false" supported_formats="*.mzML">
      </ITEMLIST>
      <ITEM name="tr" value="" type="input-file" description="transition file (&apos;TraML&apos; or &apos;csv&apos;)" required="true" advanced="false" supported_formats="*.csv,*.traML" />
      <ITEM name="rt_norm" value="" type="input-file" description="RT normalization file (how to map the RTs of this run to the ones stored in the library)" required="false" advanced="false" supported_formats="*.trafoXML" />
      <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="min_upper_edge_dist" value="0" type="double" description="Minimal distance to the edge to still consider a precursor, in Thomson" required="false" advanced="false" />
      <ITEM name="mz_window" value="0.05" type="double" description="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size, e.g. 100 ppm would extract 50 ppm on either side." required="false" advanced="false" restrictions="0:" />
      <ITEM name="rt_window" value="-1" type="double" description="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side." required="false" advanced="false" />
      <ITEM name="is_swath" value="false" type="string" description="Set this flag if the data is SWATH data" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="ppm" value="false" type="string" description="m/z extraction_window is in ppm" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="extract_MS1" value="false" type="string" description="Extract the MS1 transitions based on the precursor values in the TraML file" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="extraction_function" value="tophat" type="string" description="Function used to extract the signal" required="false" advanced="false" restrictions="tophat,bartlett" />
      <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="false" 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="model" description="Options to control the modeling of retention time transformations from data">
        <ITEM name="type" value="linear" type="string" description="Type of model" required="false" advanced="false" restrictions="linear,b_spline,interpolated" />
        <ITEM name="symmetric_regression" value="false" type="string" description="Only for &apos;linear&apos; model: Perform linear regression on &apos;y - x&apos; vs. &apos;y + x&apos;, instead of on &apos;y&apos; vs. &apos;x&apos;." required="false" advanced="false" restrictions="true,false" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
