--- a/RTModel.xml	Wed Mar 01 12:32:28 2017 -0500
+++ b/RTModel.xml	Wed Aug 09 09:19:45 2017 -0400
@@ -1,7 +1,7 @@
 <?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="2.1.0">
+<tool id="RTModel" name="RTModel" version="2.2.0">
   <description>Trains a model for the retention time prediction of peptides from a training set.</description>
   <macros>
     <token name="@EXECUTABLE@">RTModel</token>
@@ -24,8 +24,19 @@
 #if $param_out:
   -out $param_out
 #end if
+#if $param_out_oligo_params:
+  -out_oligo_params $param_out_oligo_params
+#end if
+#if $param_out_oligo_trainset:
+  -out_oligo_trainset $param_out_oligo_trainset
+#end if
 #if $param_svm_type:
-  -svm_type $param_svm_type
+  -svm_type
+  #if " " in str($param_svm_type):
+    "$param_svm_type"
+  #else
+    $param_svm_type
+  #end if
 #end if
 #if $param_nu:
   -nu $param_nu
@@ -37,7 +48,12 @@
   -c $param_c
 #end if
 #if $param_kernel_type:
-  -kernel_type $param_kernel_type
+  -kernel_type
+  #if " " in str($param_kernel_type):
+    "$param_kernel_type"
+  #else
+    $param_kernel_type
+  #end if
 #end if
 #if $param_degree:
   -degree $param_degree
@@ -124,7 +140,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="txt,idxml" optional="True" label="This is the name of the input file (RT prediction)" 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;"/>
+    <param name="param_in" type="data" format="idxml,txt" optional="True" label="This is the name of the input file (RT prediction)" 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;"/>
     <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/>
     <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/>
     <param name="param_svm_type" display="radio" type="select" optional="False" value="NU_SVR" 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)" help="(-svm_type) ">
@@ -174,6 +190,8 @@
   </inputs>
   <outputs>
     <data name="param_out" format="txt"/>
+    <data name="param_out_oligo_params" format="paramXML"/>
+    <data name="param_out_oligo_trainset" format="txt"/>
   </outputs>
   <help>Trains a model for the retention time prediction of peptides from a training set.