# HG changeset patch
# User drosofff
# Date 1499013656 14400
# Node ID 5bd8c555390d3700e6a0fdb8b9f8cabc09c0f51c
# Parent  04685a1b3de11559b287b95c60b00b3be76999e9
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty

diff -r 04685a1b3de1 -r 5bd8c555390d sRbowtie.xml
--- a/sRbowtie.xml	Sun Jul 02 12:34:18 2017 -0400
+++ b/sRbowtie.xml	Sun Jul 02 12:40:56 2017 -0400
@@ -46,11 +46,11 @@
 
         ## run the bowtie alignement
         #if $output_format == "tabular":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output
         #elif $output_format == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o $output
         #end if
         ##### | samtools view -uS
         ]]></command>