# HG changeset patch
# User greg
# Date 1515784459 18000
# Node ID c996089f1747931a7c387317f7b94f250d69b452
# Parent  b63f2ae4261a1ce49118332108316bc90682f84a
Uploaded

diff -r b63f2ae4261a -r c996089f1747 ideas.xml
--- a/ideas.xml	Fri Jan 12 14:02:27 2018 -0500
+++ b/ideas.xml	Fri Jan 12 14:14:19 2018 -0500
@@ -179,21 +179,27 @@
     #end if
 #end if
 #if str($perform_training) == "yes":
-    #set heatmaps_input_dir = $output_training_dir
     && mv ./*.para0 '$output_training_dir'
     && mv ./*.profile0 '$output_training_dir'
+    #if str($output_heatmaps) == "yes":
+        && Rscript '$__tool_directory__/create_heatmaps.R'
+        --input_dir 'input_training_dir'
+        --output_dir '$output_pdf_dir'
+        --script_dir '$__tool_directory__'
+        --training_mode true
+    #end if
+#end if
 #else:
-    #set heatmaps_input_dir = $output_txt_dir
     && mv ./*.cluster '$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 '$__tool_directory__/create_heatmaps.R'
-    --input_dir '$heatmaps_input_dir'
-    --output_dir '$output_pdf_dir'
-    --script_dir '$__tool_directory__'
+    #if str($output_heatmaps) == "yes":
+        && Rscript '$__tool_directory__/create_heatmaps.R'
+        --input_dir '$output_txt_dir'
+        --output_dir '$output_pdf_dir'
+        --script_dir '$__tool_directory__'
+    #end if
 #end if
     ]]></command>
     <configfiles>