# HG changeset patch
# User drosofff
# Date 1499013258 14400
# Node ID 04685a1b3de11559b287b95c60b00b3be76999e9
# Parent  c1ae0c9ad7d125e109ccb93eaffa84c85195364a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty

diff -r c1ae0c9ad7d1 -r 04685a1b3de1 sRbowtie.xml
--- a/sRbowtie.xml	Sun Jul 02 12:22:16 2017 -0400
+++ b/sRbowtie.xml	Sun Jul 02 12:34:18 2017 -0400
@@ -5,7 +5,7 @@
         <requirement type="package" version="1.4.1">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        #if str($refGenomeSource.genomeSource) == "history":
+        #if $refGenomeSource.genomeSource == "history":
             bowtie-build -f $refGenomeSource.ownFile local_index &&
         #else:
             ln -f -s $refGenomeSource.index.fields.path local_index &&
@@ -45,11 +45,11 @@
         #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
 
         ## run the bowtie alignement
-        #if str($output_format) == "tabular":
+        #if $output_format == "tabular":
             bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > '$output'
-        #elif str($output_format) == "sam":
+        #elif $output_format == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
-        #elif str($output_format) == "bam":
+        #elif $output_format == "bam":
             bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o '$output'
         #end if
         ##### | samtools view -uS