# HG changeset patch
# User sanbi-uwc
# Date 1527756392 14400
# Node ID fc134b9ac95129b3ae76226d5b79e69ee7f8c905
# Parent  c6e99afd59a88c96075051d8e21e68d72c268e31
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit a5e4ca4a66eb4e315ca564238e27e03936eea6fa

diff -r c6e99afd59a8 -r fc134b9ac951 novo_align.py
--- a/novo_align.py	Thu May 31 03:45:15 2018 -0400
+++ b/novo_align.py	Thu May 31 04:46:32 2018 -0400
@@ -34,7 +34,7 @@
 def main():
     parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
     parser.add_argument('out_file')
-    parser.add_argument('out_stats')    
+    parser.add_argument('--out_stats')    
     parser.add_argument('--index_filename')
     parser.add_argument('--forward_filename')
     parser.add_argument('--reverse_filename')
diff -r c6e99afd59a8 -r fc134b9ac951 novo_align.xml
--- a/novo_align.xml	Thu May 31 03:45:15 2018 -0400
+++ b/novo_align.xml	Thu May 31 04:46:32 2018 -0400
@@ -43,6 +43,7 @@
         #end if
         python $__tool_directory__/novo_align.py
             '${out_file}'
+            '${out_stats}'
             --index
             #if str($index.source) == 'builtin':
               '${index.index1.fields.path}'
@@ -123,7 +124,8 @@
         </param>
     </inputs>-->
     <outputs>
-        <data format="bam" name="out_file" />
+        <data format="sam" name="out_file" />
+        <data format="text" name="out_stats" />
     </outputs>
     <tests>
         <test>