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<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="generic_node.png" type="Manipulator">
    <name>SpectraMerger</name>
    
    <shortDescription>
        Merges spectra (each MS level separately), increasing S/N ratios.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Merges spectra (each MS level separately), increasing S/N ratios.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html">Web Documentation for SpectraMerger</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="merging_method">Method of merging which should be used.</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="mz_binning_width">minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct. Closer data points or peaks will be merged.</option>
		<option name="mz_binning_width_unit">Unit in which the distance between two data points or peaks is given.</option>
		<option name="sort_blocks">Sort blocks by &lt;?&gt; before merging them (useful for precursor order)</option>
		<option name="spectrum_type">Spectrum type of the MS level to be averaged</option>
		<option name="ms_level">Average spectra of this level. All other spectra remain unchanged.</option>
		<option name="rt_FWHM">FWHM of Gauss curve in seconds to be averaged over.</option>
		<option name="cutoff">Intensity cutoff for Gaussian. The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average.</option>
		<option name="spectrum_type">Spectrum type of the MS level to be averaged</option>
		<option name="ms_level">Average spectra of this level. All other spectra remain unchanged.</option>
		<option name="rt_range">RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.</option>
		<option name="rt_unit">Unit for RT range.</option>
		<option name="ms_levels">Merge spectra of this level. All spectra with other MS levels remain untouched.</option>
		<option name="rt_block_size">Maximum number of scans to be summed up.</option>
		<option name="rt_max_length">Maximum RT size of the block in seconds (0.0 = no size restriction).</option>
		<option name="mz_tolerance">Max m/z distance of the precursor entries of two spectra to be merged in [Da].</option>
		<option name="rt_tolerance">Max RT distance of the precursor entries of two spectra to be merged in [s].</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Input mzML file. [mzML]</inPort>
		<outPort index="0" name="out [mzML]">Output mzML file with merged spectra. [mzML]</outPort>
 </ports>
    <views>
        <view index="0" name="SpectraMerger Std Output">The text sent to standard out during the execution of SpectraMerger.</view>
        <view index="1" name="SpectraMerger Error Output">The text sent to standard error during the execution of SpectraMerger. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
