# HG changeset patch
# User drosofff
# Date 1498504703 14400
# Node ID 44d61fa7fb75304f351f588919c2cb78c4f69bf9
# Parent  a05b107fd0c40a8862660386b777e84508bf58e5
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d

diff -r a05b107fd0c4 -r 44d61fa7fb75 sRbowtie.xml
--- a/sRbowtie.xml	Mon Jun 26 12:06:12 2017 -0400
+++ b/sRbowtie.xml	Mon Jun 26 15:18:23 2017 -0400
@@ -35,20 +35,22 @@
         #if $additional_fasta == "No":
             #set extra_output = ""
         #elif $additional_fasta == "al":
-            #set extra_output = " --un %s" % str(unaligned)
+            #set extra_output = " --al %s " % str($aligned)
+        #elif $additional_fasta == "unal":
+            #set extra_output = " --un %s " % str($unaligned)
         #else:
-            #set extra_output = " --al %s --un %s" % (str($aligned), str(unaligned))
+            #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
         #end if
        
         #set $method_postfix = "$method_prefix" + "$extra_output"
 
         ## run the bowtie alignement
         #if $output_format == "tabular":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix  --suppress 6,7,8 "local_index" $format $input > $output
+            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix  --suppress 6,7,8 $extra_output$"local_index" $format $input > $output
         #elif $output_format == "sam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input > $output
+            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input > $output
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input |samtools view -bS - > $output
+            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input |samtools view -bS - > $output
         #end if
         
         ]]></command>