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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>MyriMatchAdapter</name>
    
    <shortDescription>
        Annotates MS/MS spectra using MyriMatch.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Annotates MS/MS spectra using MyriMatch.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MyriMatchAdapter.html">Web Documentation for MyriMatchAdapter</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="precursor_mass_tolerance">Precursor mono mass tolerance.</option>
		<option name="precursor_mass_tolerance_unit">Unit to be used for precursor mass tolerance.</option>
		<option name="precursor_mass_tolerance_avg">If this flag is set, the average mass is used in the precursor mass tolerance.</option>
		<option name="fragment_mass_tolerance">Fragment mass error in Dalton</option>
		<option name="fragment_mass_tolerance_unit">Unit to be used for fragment mass tolerance.</option>
		<option name="min_precursor_charge">Minimum precursor ion charge</option>
		<option name="max_precursor_charge">Maximum precursor ion charge</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="NumChargeStates">The number of charge states that MyriMatch will handle during all stages of the program.</option>
		<option name="TicCutoffPercentage">Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter.</option>
		<option name="MaxDynamicMods">This parameter sets the maximum number of modified residues that may be in any candidate sequence.</option>
		<option name="MaxResultRank">This parameter sets the maximum rank of peptide-spectrum-matches to report for each spectrum.</option>
		<option name="CleavageRules">This parameter allows the user to control the way peptides are generated from the protein database. For more details, see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&amp;termId=MS:1001045&amp;termName=cleavage%20agent%20name .</option>
		<option name="MinTerminiCleavages">By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest.</option>
		<option name="MaxMissedCleavages">By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages. A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages.</option>
		<option name="MinPeptideMass">When preprocessing the experimental spectra, any spectrum with a precursor mass that is less than the specified mass will be disqualified.</option>
		<option name="MaxPeptideMass">When preprocessing the experimental spectra, any spectrum with a precursor mass that exceeds the specified mass will be disqualified.</option>
		<option name="MinPeptideLength">When digesting proteins, any peptide which does not meet or exceed the specified length will be disqualified.</option>
		<option name="MaxPeptideLength">When digesting proteins, any peptide which exceeds this specified length will be disqualified.</option>
		<option name="UseSmartPlusThreeModel">When this parameter is set, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. The precursors protons are distributed to those ions based on that calculation, with the more basic sequence generally getting more of the protons..</option>
		<option name="NumIntensityClasses">Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this parameter.</option>
		<option name="ClassSizeMultiplier">When stratifying peaks into a specified, fixed number of intensity classes, this parameter controls the size of each class relative to the class above it (where the peaks are more intense). </option>
		<option name="MonoisotopeAdjustmentSet">This parameter defines a set of isotopes (0 being the instrument-called monoisotope) to try as the monoisotopic precursor m/z. To disable this technique, set the value to '0'.</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>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">Input file  [mzML]</inPort>
		<inPort index="1" name="database [FASTA]">FASTA protein database. [FASTA]</inPort>
		<outPort index="0" name="out [idXML]">Output file  [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="MyriMatchAdapter Std Output">The text sent to standard out during the execution of MyriMatchAdapter.</view>
        <view index="1" name="MyriMatchAdapter Error Output">The text sent to standard error during the execution of MyriMatchAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
