Mercurial > repos > zzhou > bamedit

changeset 72:ef68dddc6c64 draft

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Uploaded
author zzhou
date Mon, 26 Nov 2012 15:00:07 -0500
parents ec59db4dc58e
children 0d3c69699f0a
files bamedit.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/bamedit.xml	Mon Nov 26 15:00:01 2012 -0500
+++ b/bamedit.xml	Mon Nov 26 15:00:07 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 'printenv SCRIPT_PATH'</command>
+  <command interpreter="python">bamedit.py $options_file bash \$SCRIPT_PATH/split.sh $bamouts1 $bamouts2 $input1</command>
   <inputs>
     <conditional name="input_type">
       <param name="input_type_selector" type="select" label="Select your BAM command">