# HG changeset patch
# User iuc
# Date 1408024682 14400
# Node ID 16f7587ab084f2b3a5f82edf8140ea722e44cc4f
# Parent  106dc0bf83c64ebc5fe108e3649a32127a5735ad
Uploaded

diff -r 106dc0bf83c6 -r 16f7587ab084 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Aug 14 07:41:51 2014 -0400
+++ b/tool_dependencies.xml	Thu Aug 14 09:58:02 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="vt" version="5c735ab14b5603d9f14da6ee0e63d86ba3779934">
-      <repository changeset_revision="91635ed3dceb" name="package_vt_5c735ab14b5603d9f14da6ee0e63d86ba3779934" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="vt" version="5c735ab14b5603d9f14da6ee0e63d86ba3779934">
+        <repository changeset_revision="294fe74bded6" name="package_vt_5c735ab14b5603d9f14da6ee0e63d86ba3779934" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 106dc0bf83c6 -r 16f7587ab084 vt_normalize.xml
--- a/vt_normalize.xml	Thu Aug 14 07:41:51 2014 -0400
+++ b/vt_normalize.xml	Thu Aug 14 09:58:02 2014 -0400
@@ -11,7 +11,7 @@
         vt @BINARY@
             -o "${ outfile }"
             ##-q  do not print options and summary []
-            -w  window size for local sorting of variants [10000]
+            -w $window
 
             #if str( $intervals_file ) != 'None':
                 -I  "${intervals_file}"
@@ -20,7 +20,7 @@
             ##-i  intervals []
 
             #if $reference_source.reference_source_selector != "history":
-                -r "${reference_source.reference_genome.fields.path}"'
+                -r "${reference_source.reference_genome.fields.path}"
             #else:
                 -r "${reference_source.reference_genome}"
             #end if