# HG changeset patch
# User sanbi-uwc
# Date 1459518798 14400
# Node ID 9c51aca51902b14fa4ef44721492089f652c9e78
# Parent  a796191ac77adad354a5e9edb8b87514ae2d0c68
planemo upload for repository https://github.com/zipho/novo_sort commit c490d694fa0be39bcd5048981cf4f08cd0821a50

diff -r a796191ac77a -r 9c51aca51902 novo_sort.py
--- a/novo_sort.py	Thu Mar 31 09:58:51 2016 -0400
+++ b/novo_sort.py	Fri Apr 01 09:53:18 2016 -0400
@@ -24,6 +24,7 @@
 
 def main():
     parser = argparse.ArgumentParser(description="Re-sorting aligned files by read position")
+    parser.add_argument('output_filename')
     parser.add_argument('--bam_filename')
     args = parser.parse_args()
    
diff -r a796191ac77a -r 9c51aca51902 novo_sort.xml
--- a/novo_sort.xml	Thu Mar 31 09:58:51 2016 -0400
+++ b/novo_sort.xml	Fri Apr 01 09:53:18 2016 -0400
@@ -10,7 +10,7 @@
         <exit_code range="1:" />
     </stdio>
     <command interpreter="python">
-        novo_sort.py --bam_filename ${input1}
+        novo_sort.py '${out_file}' --bam_filename ${input1}
     </command>
     <inputs>
         <param name="input1" type="data" format="bam" label="Select first set of reads" help="Specify dataset with forward reads"/>