--- a/PTModel.xml	Wed Sep 23 15:02:13 2020 +0000
+++ b/PTModel.xml	Tue Oct 13 19:58:48 2020 +0000
@@ -21,6 +21,12 @@
 mkdir in_negative &&
 ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
 mkdir out &&
+#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_oligo_params &&
+#end if
+#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_oligo_trainset &&
+#end if
 
 ## Main program call
 
@@ -34,9 +40,26 @@
 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
 -out
 'out/output.${gxy2omsext("txt")}'
+#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_oligo_params
+  'out_oligo_params/output.${gxy2omsext("paramxml")}'
+#end if
+#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_oligo_trainset
+  'out_oligo_trainset/output.${gxy2omsext("txt")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
 
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("txt")}' '$out'
+#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
+#end if
+#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -87,17 +110,25 @@
       <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option>
+      <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
     <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
+    <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -109,6 +140,6 @@
   <help><![CDATA[Trains a model for the prediction of proteotypic peptides from a training set.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_PTModel.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PTModel.html]]></help>
   <expand macro="references"/>
 </tool>