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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>PTModel</name>
    
    <shortDescription>
        Trains a model for the prediction of proteotypic peptides from a training set.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Trains a model for the prediction of proteotypic peptides from a training set.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html">Web Documentation for PTModel</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="c">the penalty parameter of the svm</option>
		<option name="svm_type">the type of the svm (NU_SVC or C_SVC)</option>
		<option name="nu">the nu parameter [0..1] of the svm (for nu-SVR)</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="k_mer_length">k_mer length of the POBK</option>
		<option name="sigma">sigma of the POBK</option>
		<option name="max_positive_count">quantity of positive samples for training (randomly chosen if smaller than available quantity)</option>
		<option name="max_negative_count">quantity of positive samples for training (randomly chosen if smaller than available quantity)</option>
		<option name="redundant">if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be set</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">Has to be set if the cv should be skipped and the model should just be trained with the specified parameters.</option>
		<option name="number_of_runs">number of runs for the CV</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="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_positive [idXML]">input file with positive examples [idXML]</inPort>
		<inPort index="1" name="in_negative [idXML]">input file with negative examples [idXML]</inPort>
		<outPort index="0" name="out [txt]">output file: the model in libsvm format [txt]</outPort>
 </ports>
    <views>
        <view index="0" name="PTModel Std Output">The text sent to standard out during the execution of PTModel.</view>
        <view index="1" name="PTModel Error Output">The text sent to standard error during the execution of PTModel. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
