# HG changeset patch
# User drosofff
# Date 1498860765 14400
# Node ID 592eab0f31ac0254b549a7b03f0a465b71ab5df3
# Parent  2f4e22f2177d326b6e915e82c1891a019900b1e8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 5eaa99265d9ab0f4a2fbe25040c8a1e53fb82b39

diff -r 2f4e22f2177d -r 592eab0f31ac sRbowtie.xml
--- a/sRbowtie.xml	Wed Jun 28 17:45:25 2017 -0400
+++ b/sRbowtie.xml	Fri Jun 30 18:12:45 2017 -0400
@@ -50,7 +50,7 @@
         #elif $output_format == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools sort -O bam -o '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools view -uS | samtools sort -O bam -o '$output'
         #end if
         
         ]]></command>