<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.1.0" name="RTModel" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html" category="Peptide property prediction" >
<description><![CDATA[Trains a model for the retention time prediction of peptides from a training set.]]></description>
<manual><![CDATA[Trains a model for the retention time prediction of peptides from a training set.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="RTModel" description="Trains a model for the retention time prediction of peptides from a training set.">
    <ITEM name="version" value="2.1.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;RTModel&apos;">
      <ITEM name="in" value="" type="input-file" description="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#" required="false" advanced="false" supported_formats="*.idXML,*.txt" />
      <ITEM name="in_positive" value="" type="input-file" description="input file with positive examples (peptide separation prediction)#br#" required="false" advanced="false" supported_formats="*.idXML" />
      <ITEM name="in_negative" value="" type="input-file" description="input file with negative examples (peptide separation prediction)#br#" required="false" advanced="false" supported_formats="*.idXML" />
      <ITEM name="out" value="" type="output-file" description="output file: the model in libsvm format" required="true" advanced="false" supported_formats="*.txt" />
      <ITEM name="svm_type" value="NU_SVR" type="string" description="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set#br#to C_SVC for separation prediction)#br#" required="false" advanced="false" restrictions="NU_SVR,NU_SVC,EPSILON_SVR,C_SVC" />
      <ITEM name="nu" value="0.5" type="double" description="the nu parameter [0..1] of the svm (for nu-SVR)" required="false" advanced="false" restrictions="0:1" />
      <ITEM name="p" value="0.1" type="double" description="the epsilon parameter of the svm (for epsilon-SVR)" required="false" advanced="false" />
      <ITEM name="c" value="1" type="double" description="the penalty parameter of the svm" required="false" advanced="false" />
      <ITEM name="kernel_type" value="OLIGO" type="string" description="the kernel type of the svm" required="false" advanced="false" restrictions="LINEAR,RBF,POLY,OLIGO" />
      <ITEM name="degree" value="1" type="int" description="the degree parameter of the kernel function of the svm (POLY kernel)#br#" required="false" advanced="false" restrictions="1:" />
      <ITEM name="border_length" value="22" type="int" description="length of the POBK" required="false" advanced="false" restrictions="1:" />
      <ITEM name="max_std" value="10" type="double" description="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" required="false" advanced="false" restrictions="0:" />
      <ITEM name="k_mer_length" value="1" type="int" description="k_mer length of the POBK" required="false" advanced="false" restrictions="1:" />
      <ITEM name="sigma" value="5" type="double" description="sigma of the POBK" required="false" advanced="false" />
      <ITEM name="total_gradient_time" value="1" type="double" description="the time (in seconds) of the gradient (only for RT prediction)" required="false" advanced="false" restrictions="1e-05:" />
      <ITEM name="first_dim_rt" value="false" type="string" description="if set the model will be built for first_dim_rt" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="additive_cv" value="false" type="string" description="if the step sizes should be interpreted additively (otherwise the actual value is multiplied#br#with the step size to get the new value" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
      <NODE name="cv" description="Parameters for the grid search / cross validation:">
        <ITEM name="skip_cv" value="false" type="string" description="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters." required="false" advanced="false" restrictions="true,false" />
        <ITEM name="number_of_runs" value="1" type="int" description="number of runs for the CV (each run creates a new random partition of the data)" required="false" advanced="false" restrictions="1:" />
        <ITEM name="number_of_partitions" value="10" type="int" description="number of CV partitions" required="false" advanced="false" restrictions="2:" />
        <ITEM name="degree_start" value="1" type="int" description="starting point of degree" required="false" advanced="false" restrictions="1:" />
        <ITEM name="degree_step_size" value="2" type="int" description="step size point of degree" required="false" advanced="false" />
        <ITEM name="degree_stop" value="4" type="int" description="stopping point of degree" required="false" advanced="false" />
        <ITEM name="p_start" value="1" type="double" description="starting point of p" required="false" advanced="false" />
        <ITEM name="p_step_size" value="10" type="double" description="step size point of p" required="false" advanced="false" />
        <ITEM name="p_stop" value="1000" type="double" description="stopping point of p" required="false" advanced="false" />
        <ITEM name="c_start" value="1" type="double" description="starting point of c" required="false" advanced="false" />
        <ITEM name="c_step_size" value="10" type="double" description="step size of c" required="false" advanced="false" />
        <ITEM name="c_stop" value="1000" type="double" description="stopping point of c" required="false" advanced="false" />
        <ITEM name="nu_start" value="0.3" type="double" description="starting point of nu" required="false" advanced="false" restrictions="0:1" />
        <ITEM name="nu_step_size" value="1.2" type="double" description="step size of nu" required="false" advanced="false" />
        <ITEM name="nu_stop" value="0.7" type="double" description="stopping point of nu" required="false" advanced="false" restrictions="0:1" />
        <ITEM name="sigma_start" value="1" type="double" description="starting point of sigma" required="false" advanced="false" />
        <ITEM name="sigma_step_size" value="1.3" type="double" description="step size of sigma" required="false" advanced="false" />
        <ITEM name="sigma_stop" value="15" type="double" description="stopping point of sigma" required="false" advanced="false" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
