# HG changeset patch
# User rnateam
# Date 1435761663 14400
# Node ID 8c457c7a7bd747c53684eda2832259fef72ca31d
# Parent  34fc6f78ed7ccf751689ba3590aad7c70df981d4
planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty

diff -r 34fc6f78ed7c -r 8c457c7a7bd7 mea.xml
--- a/mea.xml	Wed Jul 01 10:13:10 2015 -0400
+++ b/mea.xml	Wed Jul 01 10:41:03 2015 -0400
@@ -11,20 +11,19 @@
     <exit_code range="1:" />
   </stdio>
   
-  <command><![CDATA[
-  mea
+  <command><![CDATA[mea
   #if str($mode.mode_selector) == "predict"
     $mode.dotplot
+    --alpha $mode.alpha
+    --beta $mode.beta
+    --gamma $mode.gamma
+    --delta $mode.delta
   #else
     --structure `cat $mode.structure`
   #end if
   #if str($reference) != ""
     --reference `cat $reference`
   #end if
-  --alpha $mode.alpha
-  --beta $mode.beta
-  --gamma $mode.gamma
-  --delta $mode.delta
   $slide_rule
   $conflict_rule
   > $stdout
@@ -40,8 +39,8 @@
 	<param name="dotplot" type="data" format="rna_eps" label="Dotplot"
 	       optional="false" help="Dotplot file (RNA base pair probabilities)"/>
 	<param name="alpha" label="Alpha" type="float"
-	   optional="false" value="0.012"
-	   help="Slope of base pair distance penalty"/>
+	       optional="false" value="0.012"
+	       help="Slope of base pair distance penalty"/>
 	<param name="beta" label="Beta" type="float"
 	       optional="false" value="315"
 	       help="Turning point of base pair distance penalty" />
@@ -58,7 +57,7 @@
       </when>
     </conditional>
     
-    <param name="reference" format="txt" type="data" label="Reference" />
+    <param name="reference" optional="true" format="txt" type="data" label="Reference" />
 
     <param name="slide_rule" label="Slide Rule" type="boolean"
 	   optional="false"