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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>RTPredict</name>
    
    <shortDescription>
        Predicts retention times for peptides using a model trained by RTModel.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Predicts retention times for peptides using a model trained by RTModel.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html">Web Documentation for RTPredict</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="total_gradient_time">The time (in seconds) of the gradient (peptide RT prediction)</option>
		<option name="max_number_of_peptides">The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory).</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="rewrite_peptideidentification_rtmz">Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in_id [idXML]">Peptides with precursor information [idXML,opt.]</inPort>
		<inPort index="1" name="in_text [txt]">Peptides as text-based file [txt,opt.]</inPort>
		<inPort index="2" name="svm_model [txt]">svm model in libsvm format (can be produced by RTModel) [txt]</inPort>
		<outPort index="0" name="file [idXML]">Output file with peptide RT prediction [idXML]</outPort>
		<outPort index="1" name="positive [idXML]">Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well. [idXML]</outPort>
		<outPort index="2" name="negative [idXML]">Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well. [idXML]</outPort>
		<outPort index="3" name="file [csv]">Output file with predicted RT values [csv]</outPort>
 </ports>
    <views>
        <view index="0" name="RTPredict Std Output">The text sent to standard out during the execution of RTPredict.</view>
        <view index="1" name="RTPredict Error Output">The text sent to standard error during the execution of RTPredict. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
