diff bamedit.xml @ 38:b3101aaf4ce9 draft

Uploaded

--- a/bamedit.xml	Mon Nov 26 13:27:28 2012 -0500
+++ b/bamedit.xml	Mon Nov 26 13:29:45 2012 -0500
@@ -8,7 +8,7 @@
     <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/script.sh") str("\$SCRIPT_PATH/pileup.pl")</command>
+  <command interpreter="python">bamedit.py $options_file</command>
   <inputs>
     <conditional name="input_type">
       <param name="input_type_selector" type="select" label="Select your BAM command">
@@ -73,7 +73,7 @@
 #end if
 #end if
 #if str($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), 'path':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) }