--- a/RTModel.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/RTModel.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,107 +1,193 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="RTModel" name="RTModel" version="1.12.0">
-  <description>Trains a model for the retention time prediction of peptides from a training set.</description>
-  <macros>
-    <token name="@EXECUTABLE@">RTModel</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>RTModel
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Peptide property prediction]-->
+  <tool id="RTModel" name="RTModel" version="2.0.0">
+    <description>Trains a model for the retention time prediction of peptides from a training set.</description>
+    <macros>
+      <token name="@EXECUTABLE@">RTModel</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>RTModel
 
--in ${param_in}
--in_positive ${param_in_positive}
--in_negative ${param_in_negative}
--out ${param_out}
--svm_type ${param_svm_type}
--nu ${param_nu}
--p ${param_p}
--c ${param_c}
--kernel_type ${param_kernel_type}
--degree ${param_degree}
--border_length ${param_border_length}
--max_std ${param_max_std}
--k_mer_length ${param_k_mer_length}
--sigma ${param_sigma}
--total_gradient_time ${param_total_gradient_time}
-${param_first_dim_rt}
-${param_additive_cv}
--threads \${GALAXY_SLOTS:-24} 
-${param_skip_cv}
--cv:number_of_runs ${param_number_of_runs}
--cv:number_of_partitions ${param_number_of_partitions}
--cv:degree_start ${param_degree_start}
--cv:degree_step_size ${param_degree_step_size}
--cv:degree_stop ${param_degree_stop}
--cv:p_start ${param_p_start}
--cv:p_step_size ${param_p_step_size}
--cv:p_stop ${param_p_stop}
--cv:c_start ${param_c_start}
--cv:c_step_size ${param_c_step_size}
--cv:c_stop ${param_c_stop}
--cv:nu_start ${param_nu_start}
--cv:nu_step_size ${param_nu_step_size}
--cv:nu_stop ${param_nu_stop}
--cv:sigma_start ${param_sigma_start}
--cv:sigma_step_size ${param_sigma_step_size}
--cv:sigma_stop ${param_sigma_stop}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_in_positive:
+  -in_positive $param_in_positive
+#end if
+#if $param_in_negative:
+  -in_negative $param_in_negative
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_svm_type:
+  -svm_type
+  #if &quot; &quot; in str($param_svm_type):
+    &quot;$param_svm_type&quot;
+  #else
+    $param_svm_type
+  #end if
+#end if
+#if $param_nu:
+  -nu $param_nu
+#end if
+#if $param_p:
+  -p $param_p
+#end if
+#if $param_c:
+  -c $param_c
+#end if
+#if $param_kernel_type:
+  -kernel_type
+  #if &quot; &quot; in str($param_kernel_type):
+    &quot;$param_kernel_type&quot;
+  #else
+    $param_kernel_type
+  #end if
+#end if
+#if $param_degree:
+  -degree $param_degree
+#end if
+#if $param_border_length:
+  -border_length $param_border_length
+#end if
+#if $param_max_std:
+  -max_std $param_max_std
+#end if
+#if $param_k_mer_length:
+  -k_mer_length $param_k_mer_length
+#end if
+#if $param_sigma:
+  -sigma $param_sigma
+#end if
+#if $param_total_gradient_time:
+  -total_gradient_time $param_total_gradient_time
+#end if
+#if $param_first_dim_rt:
+  -first_dim_rt
+#end if
+#if $param_additive_cv:
+  -additive_cv
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_cv_skip_cv:
+  -cv:skip_cv
+#end if
+#if $param_cv_number_of_runs:
+  -cv:number_of_runs $param_cv_number_of_runs
+#end if
+#if $param_cv_number_of_partitions:
+  -cv:number_of_partitions $param_cv_number_of_partitions
+#end if
+#if $param_cv_degree_start:
+  -cv:degree_start $param_cv_degree_start
+#end if
+#if $param_cv_degree_step_size:
+  -cv:degree_step_size $param_cv_degree_step_size
+#end if
+#if $param_cv_degree_stop:
+  -cv:degree_stop $param_cv_degree_stop
+#end if
+#if $param_cv_p_start:
+  -cv:p_start $param_cv_p_start
+#end if
+#if $param_cv_p_step_size:
+  -cv:p_step_size $param_cv_p_step_size
+#end if
+#if $param_cv_p_stop:
+  -cv:p_stop $param_cv_p_stop
+#end if
+#if $param_cv_c_start:
+  -cv:c_start $param_cv_c_start
+#end if
+#if $param_cv_c_step_size:
+  -cv:c_step_size $param_cv_c_step_size
+#end if
+#if $param_cv_c_stop:
+  -cv:c_stop $param_cv_c_stop
+#end if
+#if $param_cv_nu_start:
+  -cv:nu_start $param_cv_nu_start
+#end if
+#if $param_cv_nu_step_size:
+  -cv:nu_step_size $param_cv_nu_step_size
+#end if
+#if $param_cv_nu_stop:
+  -cv:nu_stop $param_cv_nu_stop
+#end if
+#if $param_cv_sigma_start:
+  -cv:sigma_start $param_cv_sigma_start
+#end if
+#if $param_cv_sigma_step_size:
+  -cv:sigma_step_size $param_cv_sigma_step_size
+#end if
+#if $param_cv_sigma_stop:
+  -cv:sigma_stop $param_cv_sigma_stop
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="idXML,txt" optional="True" label="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#" help="(-in)"/>
-    <param name="param_in_positive" type="data" format="idXML" optional="True" label="input file with positive examples (peptide separation prediction)#br#" help="(-in_positive)"/>
-    <param name="param_in_negative" type="data" format="idXML" optional="True" label="input file with negative examples (peptide separation prediction)#br#" help="(-in_negative)"/>
-    <param name="param_svm_type" type="select" optional="True" value="NU_SVR" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set#br#to C_SVC for separation prediction)#br#" help="(-svm_type)">
-      <option value="NU_SVR">NU_SVR</option>
-      <option value="NU_SVC">NU_SVC</option>
-      <option value="EPSILON_SVR">EPSILON_SVR</option>
-      <option value="C_SVC">C_SVC</option>
-    </param>
-    <param name="param_nu" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help="(-nu)"/>
-    <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p)"/>
-    <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c)"/>
-    <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type)">
-      <option value="LINEAR">LINEAR</option>
-      <option value="RBF">RBF</option>
-      <option value="POLY">POLY</option>
-      <option value="OLIGO">OLIGO</option>
-    </param>
-    <param name="param_degree" type="integer" min="1" optional="True" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)#br#" help="(-degree)"/>
-    <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length)"/>
-    <param name="param_max_std" type="float" min="0.0" optional="True" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help="(-max_std)"/>
-    <param name="param_k_mer_length" type="integer" min="1" optional="True" value="1" label="k_mer length of the POBK" help="(-k_mer_length)"/>
-    <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma)"/>
-    <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help="(-total_gradient_time)"/>
-    <param name="param_first_dim_rt" type="boolean" truevalue="-first_dim_rt true" falsevalue="-first_dim_rt false" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt)"/>
-    <param name="param_additive_cv" type="boolean" truevalue="-additive_cv true" falsevalue="-additive_cv false" checked="false" optional="True" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied#br#with the step size to get the new value" help="(-additive_cv)"/>
-    <param name="param_skip_cv" type="boolean" truevalue="-cv:skip_cv true" falsevalue="-cv:skip_cv false" checked="false" optional="True" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters." help="(-skip_cv)"/>
-    <param name="param_number_of_runs" type="integer" min="1" optional="True" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help="(-number_of_runs)"/>
-    <param name="param_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions)"/>
-    <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/>
-    <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/>
-    <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/>
-    <param name="param_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start)"/>
-    <param name="param_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size)"/>
-    <param name="param_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop)"/>
-    <param name="param_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start)"/>
-    <param name="param_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size)"/>
-    <param name="param_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop)"/>
-    <param name="param_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start)"/>
-    <param name="param_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size)"/>
-    <param name="param_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="stopping point of nu" help="(-nu_stop)"/>
-    <param name="param_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start)"/>
-    <param name="param_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size)"/>
-    <param name="param_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file: the model in libsvm format" format="txt"/>
-  </outputs>
-  <help>**What it does**
-
-Trains a model for the retention time prediction of peptides from a training set.
+    <inputs>
+      <param format="xml,txt" help="(-in) 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. &lt;br&gt;" label="This is the name of the input file (RT prediction)" name="param_in" optional="True" type="data"/>
+      <param format="xml" help="(-in_positive) " label="input file with positive examples (peptide separation prediction)" name="param_in_positive" optional="True" type="data"/>
+      <param format="xml" help="(-in_negative) " label="input file with negative examples (peptide separation prediction)" name="param_in_negative" optional="True" type="data"/>
+      <param help="(-svm_type) " label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set &lt;br&gt;to C_SVC for separation prediction)" name="param_svm_type" optional="True" type="select" value="NU_SVR">
+        <option value="NU_SVR">NU_SVR</option>
+        <option value="NU_SVC">NU_SVC</option>
+        <option value="EPSILON_SVR">EPSILON_SVR</option>
+        <option value="C_SVC">C_SVC</option>
+      </param>
+      <param help="(-nu) " label="the nu parameter [0..1] of the svm (for nu-SVR)" max="1.0" min="0.0" name="param_nu" optional="True" type="float" value="0.5"/>
+      <param help="(-p) " label="the epsilon parameter of the svm (for epsilon-SVR)" name="param_p" type="float" value="0.1"/>
+      <param help="(-c) " label="the penalty parameter of the svm" name="param_c" type="float" value="1.0"/>
+      <param help="(-kernel_type) " label="the kernel type of the svm" name="param_kernel_type" optional="True" type="select" value="OLIGO">
+        <option value="LINEAR">LINEAR</option>
+        <option value="RBF">RBF</option>
+        <option value="POLY">POLY</option>
+        <option value="OLIGO">OLIGO</option>
+      </param>
+      <param help="(-degree) " label="the degree parameter of the kernel function of the svm (POLY kernel)" min="1" name="param_degree" optional="True" type="integer" value="1"/>
+      <param help="(-border_length) " label="length of the POBK" min="1" name="param_border_length" optional="True" type="integer" value="22"/>
+      <param help="(-max_std) " label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" min="0.0" name="param_max_std" optional="True" type="float" value="10.0"/>
+      <param help="(-k_mer_length) " label="k_mer length of the POBK" min="1" name="param_k_mer_length" optional="True" type="integer" value="1"/>
+      <param help="(-sigma) " label="sigma of the POBK" name="param_sigma" type="float" value="5.0"/>
+      <param help="(-total_gradient_time) " label="the time (in seconds) of the gradient (only for RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
+      <param checked="false" falsevalue="" help="(-first_dim_rt) " label="if set the model will be built for first_dim_rt" name="param_first_dim_rt" optional="True" truevalue="-first_dim_rt" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-additive_cv) " label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied &lt;br&gt;with the step size to get the new value" name="param_additive_cv" optional="True" truevalue="-additive_cv" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-skip_cv) " label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" name="param_cv_skip_cv" optional="True" truevalue="-cv:skip_cv" type="boolean"/>
+      <param help="(-number_of_runs) " label="number of runs for the CV (each run creates a new random partition of the data)" min="1" name="param_cv_number_of_runs" optional="True" type="integer" value="1"/>
+      <param help="(-number_of_partitions) " label="number of CV partitions" min="2" name="param_cv_number_of_partitions" optional="True" type="integer" value="10"/>
+      <param help="(-degree_start) " label="starting point of degree" min="1" name="param_cv_degree_start" optional="True" type="integer" value="1"/>
+      <param help="(-degree_step_size) " label="step size point of degree" name="param_cv_degree_step_size" type="integer" value="2"/>
+      <param help="(-degree_stop) " label="stopping point of degree" name="param_cv_degree_stop" type="integer" value="4"/>
+      <param help="(-p_start) " label="starting point of p" name="param_cv_p_start" type="float" value="1.0"/>
+      <param help="(-p_step_size) " label="step size point of p" name="param_cv_p_step_size" type="float" value="10.0"/>
+      <param help="(-p_stop) " label="stopping point of p" name="param_cv_p_stop" type="float" value="1000.0"/>
+      <param help="(-c_start) " label="starting point of c" name="param_cv_c_start" type="float" value="1.0"/>
+      <param help="(-c_step_size) " label="step size of c" name="param_cv_c_step_size" type="float" value="10.0"/>
+      <param help="(-c_stop) " label="stopping point of c" name="param_cv_c_stop" type="float" value="1000.0"/>
+      <param help="(-nu_start) " label="starting point of nu" max="1.0" min="0.0" name="param_cv_nu_start" optional="True" type="float" value="0.3"/>
+      <param help="(-nu_step_size) " label="step size of nu" name="param_cv_nu_step_size" type="float" value="1.2"/>
+      <param help="(-nu_stop) " label="stopping point of nu" max="1.0" min="0.0" name="param_cv_nu_stop" optional="True" type="float" value="0.7"/>
+      <param help="(-sigma_start) " label="starting point of sigma" name="param_cv_sigma_start" type="float" value="1.0"/>
+      <param help="(-sigma_step_size) " label="step size of sigma" name="param_cv_sigma_step_size" type="float" value="1.3"/>
+      <param help="(-sigma_stop) " label="stopping point of sigma" name="param_cv_sigma_stop" type="float" value="15.0"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="txt" name="param_out"/>
+    </outputs>
+    <help>Trains a model for the retention time prediction of peptides from a training set.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>
+  </tool>