# HG changeset patch
# User drosofff
# Date 1498862795 14400
# Node ID 405cd77e5a831c16d9809c38f981935769a948de
# Parent  592eab0f31ac0254b549a7b03f0a465b71ab5df3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 49b9fd4b6b28a6cbbabc6fa0356cf52be20b7a3e

diff -r 592eab0f31ac -r 405cd77e5a83 sRbowtie.xml
--- a/sRbowtie.xml	Fri Jun 30 18:12:45 2017 -0400
+++ b/sRbowtie.xml	Fri Jun 30 18:46:35 2017 -0400
@@ -45,11 +45,11 @@
         #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
 
         ## run the bowtie alignement
-        #if $output_format == "tabular":
+        #if str($output_format) == "tabular":
             bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' --suppress 6,7,8 '$extra_output' local_index '$format' '$input' > '$output'
-        #elif $output_format == "sam":
+        #elif str($output_format) == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output
-        #elif $output_format == "bam":
+        #elif str($output_format) == "bam":
             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