# HG changeset patch
# User zzhou
# Date 1353958022 18000
# Node ID 4ebe0aa42cf005cc6cadb99c1e174ce945883f7c
# Parent  ad92d59fb5e297d916fe26cf636d9f8f0abb997a
Uploaded

diff -r ad92d59fb5e2 -r 4ebe0aa42cf0 bamedit.xml
--- a/bamedit.xml	Mon Nov 26 14:26:55 2012 -0500
+++ b/bamedit.xml	Mon Nov 26 14:27:02 2012 -0500
@@ -9,7 +9,7 @@
     <requirement type="package" version="0.1.12">samtools</requirement>
   </requirements>
   <description>Merging, splitting, filtering, and QC of BAM files</description>
-  <command interpreter="python">bamedit.py $options_file str(\$SCRIPT_PATH)</command>
+  <command interpreter="python">bamedit.py $options_file '\SCRIPT_PATH'</command>
   <inputs>
     <conditional name="input_type">
       <param name="input_type_selector" type="select" label="Select your BAM command">
@@ -74,7 +74,7 @@
 #end if
 #end if
 #if str($input_type.input_type_selector) == 'split':
-#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
+#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1), 'testing':str('\$SCRIPT_PATH') }
 #end if
 #if str($input_type.input_type_selector) == 'filter':
 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }