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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>MassCalculator</name>
    
    <shortDescription>
        Calculates masses and mass-to-charge ratios of peptide sequences
    </shortDescription>
    
    <fullDescription>
        <intro><p>Calculates masses and mass-to-charge ratios of peptide sequences</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html">Web Documentation for MassCalculator</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="in_seq">List of peptide sequences (mutually exclusive to 'in')</option>
		<option name="charge">List of charge states; required if 'in_seq' is given</option>
		<option name="format">Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)
</option>
		<option name="average_mass">Compute average (instead of monoisotopic) peptide masses</option>
		<option name="fragment_type">For what type of sequence/fragment the mass should be computed
</option>
		<option name="separator">Field separator for 'table' output format; by default, the 'tab' character is 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>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [txt]">Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq') [txt,opt.]</inPort>
		<outPort index="0" name="out [txt,Inactive]">Output file; if empty, output is written to the screen [txt,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="MassCalculator Std Output">The text sent to standard out during the execution of MassCalculator.</view>
        <view index="1" name="MassCalculator Error Output">The text sent to standard error during the execution of MassCalculator. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
