diff bamedit.xml @ 44:80871d2d80a4 draft

Uploaded

--- a/bamedit.xml	Mon Nov 26 13:37:30 2012 -0500
+++ b/bamedit.xml	Mon Nov 26 13:37:36 2012 -0500
@@ -5,10 +5,11 @@
 -->
 <tool id="BAM_Editor" name="BAMEdit" version="1.1.0">
   <requirements>
+    <requirement type="set_enviornment">SCRIPT_PATH</requirement>
     <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</command>
+  <command interpreter="python">bamedit.py $options_file $SCRIPT_PATH</command>
   <inputs>
     <conditional name="input_type">
       <param name="input_type_selector" type="select" label="Select your BAM command">
@@ -73,7 +74,7 @@
 #end if
 #end if
 #if str($input_type.input_type_selector) == 'split':
-#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1), 'spath':str(\$SCRIPT_PATH) }
+#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
 #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) }