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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>RTModel</name>
    
    <shortDescription>
        Trains a model for the retention time prediction of peptides from a training set.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Trains a model for the retention time prediction of peptides from a training set.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html">Web Documentation for RTModel</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="svm_type">the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set
to C_SVC for separation prediction)
</option>
		<option name="nu">the nu parameter [0..1] of the svm (for nu-SVR)</option>
		<option name="p">the epsilon parameter of the svm (for epsilon-SVR)</option>
		<option name="c">the penalty parameter of the svm</option>
		<option name="kernel_type">the kernel type of the svm</option>
		<option name="degree">the degree parameter of the kernel function of the svm (POLY kernel)
</option>
		<option name="border_length">length of the POBK</option>
		<option name="max_std">max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)</option>
		<option name="k_mer_length">k_mer length of the POBK</option>
		<option name="sigma">sigma of the POBK</option>
		<option name="total_gradient_time">the time (in seconds) of the gradient (only for RT prediction)</option>
		<option name="first_dim_rt">if set the model will be built for first_dim_rt</option>
		<option name="additive_cv">if the step sizes should be interpreted additively (otherwise the actual value is multiplied
with the step size to get the new value</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="skip_cv">Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters.</option>
		<option name="number_of_runs">number of runs for the CV (each run creates a new random partition of the data)</option>
		<option name="number_of_partitions">number of CV partitions</option>
		<option name="degree_start">starting point of degree</option>
		<option name="degree_step_size">step size point of degree</option>
		<option name="degree_stop">stopping point of degree</option>
		<option name="p_start">starting point of p</option>
		<option name="p_step_size">step size point of p</option>
		<option name="p_stop">stopping point of p</option>
		<option name="c_start">starting point of c</option>
		<option name="c_step_size">step size of c</option>
		<option name="c_stop">stopping point of c</option>
		<option name="nu_start">starting point of nu</option>
		<option name="nu_step_size">step size of nu</option>
		<option name="nu_stop">stopping point of nu</option>
		<option name="sigma_start">starting point of sigma</option>
		<option name="sigma_step_size">step size of sigma</option>
		<option name="sigma_stop">stopping point of sigma</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [idXML,txt]">This is the name of the input file (RT prediction). It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line.#br# [idXML,txt,opt.]</inPort>
		<inPort index="1" name="in_positive [idXML]">input file with positive examples (peptide separation prediction)#br# [idXML,opt.]</inPort>
		<inPort index="2" name="in_negative [idXML]">input file with negative examples (peptide separation prediction)#br# [idXML,opt.]</inPort>
		<outPort index="0" name="out [txt]">output file: the model in libsvm format [txt]</outPort>
 </ports>
    <views>
        <view index="0" name="RTModel Std Output">The text sent to standard out during the execution of RTModel.</view>
        <view index="1" name="RTModel Error Output">The text sent to standard error during the execution of RTModel. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
