# HG changeset patch
# User drosofff
# Date 1498551704 14400
# Node ID f752a90d266f2e501ce94d4c7d36277c903e1fc5
# Parent  ffe2430ef56dfedbeab5563ad032ab98315c0587
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 2759e9b0ec00022871f493fb43540c5602f74a5a

diff -r ffe2430ef56d -r f752a90d266f sRbowtie.xml
--- a/sRbowtie.xml	Mon Jun 26 20:02:27 2017 -0400
+++ b/sRbowtie.xml	Tue Jun 27 04:21:44 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 $extra_output "local_index" $format $input > $output
+            bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' --suppress 6,7,8 '${extra_output}' local_index '${format}' '$input' > '$output'
         #elif $output_format == "sam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix $extra_output -S "local_index" $format $input > $output
+            bowtie -p \${GALAXY_SLOTS:-4} '${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 view -bS - > $output
+            bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input |samtools view -bS - > $output
         #end if
         
         ]]></command>