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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>CompNovo</name>
    
    <shortDescription>
        Performs a de novo peptide identification using the CompNovo engine.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Performs a de novo peptide identification using the CompNovo engine.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovo.html">Web Documentation for CompNovo</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</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="max_number_aa_per_decomp">maximal amino acid frequency per decomposition</option>
		<option name="tryptic_only">if set to true only tryptic peptides are reported</option>
		<option name="precursor_mass_tolerance">precursor mass tolerance</option>
		<option name="fragment_mass_tolerance">fragment mass tolerance</option>
		<option name="max_number_pivot">maximal number of pivot ions to be used</option>
		<option name="max_subscore_number">maximal number of solutions of a subsegment that are kept</option>
		<option name="decomp_weights_precision">precision used to calculate the decompositions, this only affects cache usage!</option>
		<option name="double_charged_iso_threshold">minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions</option>
		<option name="max_mz">maximal m/z value used to calculate isotope distributions</option>
		<option name="min_mz">minimal m/z value used to calculate the isotope distributions</option>
		<option name="max_isotope_to_score">max isotope peak to be considered in the scoring</option>
		<option name="max_decomp_weight">maximal m/z difference used to calculate the decompositions</option>
		<option name="max_isotope">max isotope used in the theoretical spectra to score</option>
		<option name="missed_cleavages">maximal number of missed cleavages allowed per peptide</option>
		<option name="number_of_hits">maximal number of hits which are reported per spectrum</option>
		<option name="estimate_precursor_mz">If set to true, the precursor charge will be estimated, e.g. from the precursor peaks of the ETD spectrum.#br#The input is believed otherwise.</option>
		<option name="number_of_prescoring_hits">how many sequences are kept after first rough scoring for better scoring</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="residue_set">The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">input file in mzML format [mzML]</inPort>
		<outPort index="0" name="out [idXML]">output file in idXML format [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="CompNovo Std Output">The text sent to standard out during the execution of CompNovo.</view>
        <view index="1" name="CompNovo Error Output">The text sent to standard error during the execution of CompNovo. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
