# HG changeset patch
# User drosofff
# Date 1498520965 14400
# Node ID 9fe34d55bfb058bb4a37dbdc2690a9b03d37ecee
# Parent  0806b5d0b5da2c65ddc29697f4d784ea05e48ba1
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 083e56a5896485479dfd679e0b571eb2bd8aed0b

diff -r 0806b5d0b5da -r 9fe34d55bfb0 sRbowtie.xml
--- a/sRbowtie.xml	Mon Jun 26 19:37:53 2017 -0400
+++ b/sRbowtie.xml	Mon Jun 26 19:49:25 2017 -0400
@@ -8,7 +8,7 @@
         #if $refGenomeSource.genomeSource == "history":
             bowtie-build -f '$refGenomeSource.ownFile' local_index &&
         #else:
-            ln -s local_index '$refGenomeSource.index.fields.path' &&
+            ln -f -s '$refGenomeSource.index.fields.path' local_index &&
         #end if
         #if $input.extension == "fasta":
             #set format = "-f"
@@ -42,15 +42,15 @@
             #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
         #end if
        
-        #set $method_postfix = "$method_prefix" + "$extra_output"
+        #set $method_postfix = " %s %s " % ($method_prefix", "$extra_output")
 
         ## run the bowtie alignement
         #if $output_format == "tabular":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix  --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_prefix $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_prefix $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>