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    <name>SpecLibSearcher</name>
    
    <shortDescription>
        Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpecLibSearcher.html">Web Documentation for SpecLibSearcher</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="precursor_mass_tolerance">Precursor mass tolerance, (Th)</option>
		<option name="round_precursor_to_integer">many precursor m/z multipling number lead to the same number; are packed in the same vector for faster search.Should be higher for high-resolution data</option>
		<option name="compare_function">function for similarity comparisson</option>
		<option name="top_hits">save the first &lt;number&gt; top hits. For all type -1</option>
		<option name="fixed_modifications">fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</option>
		<option name="variable_modifications">variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</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="remove_peaks_below_threshold">All peaks of a query spectrum with intensities below &lt;threshold&gt; will be zeroed.</option>
		<option name="min_peaks">required mininum number of peaks for a query spectrum</option>
		<option name="max_peaks">Use only the top &lt;number&gt; of peaks.</option>
		<option name="cut_peaks_below">Remove all peaks which are lower than 1/&lt;number&gt; of the highest peaks. Default equals all peaks which are lower than 0.001 of the maximum intensity peak</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Input files [mzML]</inPort>
		<inPort index="1" name="lib [msp]">searchable spectral library (MSP format) [msp]</inPort>
		<outPort index="0" name="out [idXML]">Output files. Have to be as many as input files [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="SpecLibSearcher Std Output">The text sent to standard out during the execution of SpecLibSearcher.</view>
        <view index="1" name="SpecLibSearcher Error Output">The text sent to standard error during the execution of SpecLibSearcher. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
