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    <name>OpenSwathChromatogramExtractor</name>
    
    <shortDescription>
        Extract chromatograms (XIC) from a MS2 map file.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Extract chromatograms (XIC) from a MS2 map file.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html">Web Documentation for OpenSwathChromatogramExtractor</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="min_upper_edge_dist">Minimal distance to the edge to still consider a precursor, in Thomson</option>
		<option name="mz_window">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.</option>
		<option name="rt_window">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.</option>
		<option name="is_swath">Set this flag if the data is SWATH data</option>
		<option name="ppm">m/z extraction_window is in ppm</option>
		<option name="extract_MS1">Extract the MS1 transitions based on the precursor values in the TraML file</option>
		<option name="extraction_function">Function used to extract the signal</option>
		<option name="log">Name of log file (created only when specified)</option>
		<option name="debug">Sets the debug level</option>
		<option name="threads">Sets the number of threads allowed to be used by the TOPP tool</option>
		<option name="no_progress">Disables progress logging to command line</option>
		<option name="force">Overwrite tool specific checks.</option>
		<option name="test">Enables the test mode (needed for internal use only)</option>
		<option name="type">Type of model</option>
		<option name="symmetric_regression">Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Input files separated by blank [mzML]</inPort>
		<inPort index="1" name="tr [csv,traML]">transition file ('TraML' or 'csv') [csv,traML]</inPort>
		<inPort index="2" name="rt_norm [trafoXML]">RT normalization file (how to map the RTs of this run to the ones stored in the library) [trafoXML,opt.]</inPort>
		<outPort index="0" name="out [mzML]">output file [mzML]</outPort>
 </ports>
    <views>
        <view index="0" name="OpenSwathChromatogramExtractor Std Output">The text sent to standard out during the execution of OpenSwathChromatogramExtractor.</view>
        <view index="1" name="OpenSwathChromatogramExtractor Error Output">The text sent to standard error during the execution of OpenSwathChromatogramExtractor. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
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