Mercurial > repos > devteam > bwa

diff bwa.xml @ 12:bd3a1e0de84c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author: devteam
date: Fri, 30 Dec 2016 08:11:12 -0500
parents: 546ada4a9f43
children: 53646aaaafef
--- a/bwa.xml	Tue Jan 19 11:20:59 2016 -0500
+++ b/bwa.xml	Fri Dec 30 08:11:12 2016 -0500
@@ -218,9 +218,7 @@
       "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
     #end if
 
-    | samtools view -Sb - > temporary_bam_file.bam &&
-
-    samtools sort -f temporary_bam_file.bam ${bam_output}
+    | samtools sort -O bam -o '$bam_output'
 ]]>
   </command>