From a08c0c03ce2f3927e3181d75f0368ad72f8b8ea1 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 8 Jun 2012 13:48:37 -0400
Subject: [PATCH] Fix bug in setting Bowtie2 parameters.

---
 tools/sr_mapping/bowtie2_wrapper.xml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tools/sr_mapping/bowtie2_wrapper.xml b/tools/sr_mapping/bowtie2_wrapper.xml
index 4e26d8437c0..35bfff9fce5 100644
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -35,10 +35,12 @@
         ## Set params.
         --settings=$params.settingsType
         
-        #if str($params.align_type) == "end_to_end":
-            --end-to-end --preset-alignment=$params.preset.align_preset_select
-        #else:
-            --local --preset-alignment=$params.preset.align_preset_select-local
+        #if $params.settingsType == "full":
+            #if str($params.align_type) == "end_to_end":
+                --end-to-end --preset-alignment=$params.preset.align_preset_select
+            #else:
+                --local --preset-alignment=$params.preset.align_preset_select-local
+            #end if
         #end if
     </command>
     <inputs>