# HG changeset patch
# User rnateam
# Date 1435762229 14400
# Node ID 00e0ba24886ae371eb0d153e2cdcd963ed6e817a
# Parent  8c457c7a7bd747c53684eda2832259fef72ca31d
planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty

diff -r 8c457c7a7bd7 -r 00e0ba24886a mea.xml
--- a/mea.xml	Wed Jul 01 10:41:03 2015 -0400
+++ b/mea.xml	Wed Jul 01 10:50:29 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="mea" name="MEA" version="0.6.4.0">
+<tool id="mea" name="MEA" version="0.6.4.1">
   <description>Predict maximum expected accuracy secondary structures
   of RNAs and compare RNA secondary structures</description>
   
@@ -21,11 +21,11 @@
   #else
     --structure `cat $mode.structure`
   #end if
-  #if str($reference) != ""
+  #if $mode.compare == "compare"
     --reference `cat $reference`
+    $slide_rule
+    $conflict_rule
   #end if
-  $slide_rule
-  $conflict_rule
   > $stdout
   ]]></command>
   
diff -r 8c457c7a7bd7 -r 00e0ba24886a tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 01 10:41:03 2015 -0400
+++ b/tool_dependencies.xml	Wed Jul 01 10:50:29 2015 -0400
@@ -19,10 +19,8 @@
               <action type="autoconf" />
 	      
               <action type="set_environment">
-                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin
-		</environment_variable>
-		<environment_variable action="set_to" name="MEA_ROOT_PATH">$INSTALL_DIR
-		</environment_variable>
+                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+		<environment_variable action="set_to" name="MEA_ROOT_PATH">$INSTALL_DIR</environment_variable>
               </action>
             </actions>
         </install>