--- a/ideas.xml	Fri Jan 12 13:12:47 2018 -0500
+++ b/ideas.xml	Fri Jan 12 13:43:08 2018 -0500
@@ -12,6 +12,7 @@
     <command detect_errors="exit_code"><![CDATA[
 #set output_pdf_dir = "output_pdf_dir"
 #set output_txt_dir = "output_txt_dir"
+#set output_txt_dir = "output_training_dir"
 #set tmp_dir = "tmp"
 #set prep_input_config = "prep_input_config.txt"
 #set prep_output_config = "prep_output_config.txt"
@@ -23,6 +24,9 @@
 #if str($output_heatmaps) == "yes":
     mkdir '$output_pdf_dir' &&
 #end if
+#if str($perform_training) == "yes":
+    mkdir '$output_training_dir' &&
+#end if
 mkdir '$output_txt_dir' &&
 cp '$gen_prep_input_config' $prep_input_config &&
 sort $prep_input_config -o $prep_input_config &&
@@ -174,10 +178,15 @@
         --output_log '$output_log'
     #end if
 #end if
-&& mv ./*.cluster '$output_txt_dir'
-&& mv ./*.para '$output_txt_dir'
-&& mv ./*.profile '$output_txt_dir'
-&& mv ./*.state '$output_txt_dir'
+#if str($perform_training) == "yes":
+    && mv ./*.para0 '$output_training_dir'
+    && mv ./*.profile0 '$output_training_dir'
+#else:
+    && mv ./*.cluster '$output_txt_dir'
+    && mv ./*.para '$output_txt_dir'
+    && mv ./*.profile '$output_txt_dir'
+    && mv ./*.state '$output_txt_dir'
+#end if
 #if str($output_heatmaps) == "yes":
     && Rscript '$__tool_directory__/create_heatmaps.R'
     --input_dir '$output_txt_dir'
@@ -217,8 +226,8 @@
                 <option value="no">No</option>
             </param>
             <when value="yes">
-                <param name="training_iterations" type="integer" value="20" min="1" label="Number of training iterations"/>
-                <param name="training_windows" type="integer" value="10000" min="1" label="Number of randomly selected windows for training"/>
+                <param name="training_iterations" type="integer" value="20" min="2" label="Number of training iterations"/>
+                <param name="training_windows" type="integer" value="10000" min="2" label="Number of randomly selected windows for training"/>
             </when>
             <when value="no"/>
         </conditional>
@@ -317,6 +326,11 @@
         </collection>
         <collection name="output_txt_collection" type="list">
             <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/>
+            <filter>perform_training_cond['perform_training'] == 'no'</filter>
+        </collection>
+        <collection name="output_ttraining_collection" type="list">
+            <discover_datasets pattern="__name__" directory="output_training_dir" format="txt"/>
+            <filter>perform_training_cond['perform_training'] == 'yes'</filter>
         </collection>
     </outputs>
     <tests>