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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>DecoyDatabase</name>
    
    <shortDescription>
        Create decoy peptide databases from normal ones.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Create decoy peptide databases from normal ones.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html">Web Documentation for DecoyDatabase</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="decoy_string">String that is combined with the accession of the protein identifier to indicate a decoy protein.</option>
		<option name="decoy_string_position">Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?</option>
		<option name="append">If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches.</option>
		<option name="method">Method by which decoy sequences are generated from target sequences.</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 [fasta]">Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well. [fasta]</inPort>
		<outPort index="0" name="out [fasta]">Output FASTA file where the decoy database will be written to. [fasta]</outPort>
 </ports>
    <views>
        <view index="0" name="DecoyDatabase Std Output">The text sent to standard out during the execution of DecoyDatabase.</view>
        <view index="1" name="DecoyDatabase Error Output">The text sent to standard error during the execution of DecoyDatabase. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
