Mercurial > repos > iuc > vt_variant_tools

diff vt_normalize.xml @ 6:d67bfd79bf6c draft default tip

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Uploaded
author bgruening
date Thu, 14 Aug 2014 12:37:17 -0400
parents b425a93b4da6
children
line wrap: on
line diff
--- a/vt_normalize.xml	Thu Aug 14 10:44:32 2014 -0400
+++ b/vt_normalize.xml	Thu Aug 14 12:37:17 2014 -0400
@@ -9,7 +9,7 @@
     <command>
 <![CDATA[
         vt @BINARY@
-            #if $output_format == 'bcf':
+            #if str($output_format) == 'bcf':
                 -o normalised.bcf
             #else:
                 -o normalised.vcf
@@ -29,9 +29,11 @@
                 -r "${reference_source.reference_genome}"
             #end if
 
-            "${ infile }";
+            "${ infile }"
 
-        #if $output_format == 'bcf':
+        &&
+
+        #if str($output_format) == 'bcf':
             mv normalised.bcf "${ outfile }";
         #else:
             mv normalised.vcf "${ outfile }";