# HG changeset patch
# User devteam
# Date 1437498051 14400
# Node ID 1fc845afa3acdcba0cebd6c0f07f15b4263f38b9
# Parent  ceb6467e276c0cdb3612a80a59fc5dd7dd43b2f7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty

diff -r ceb6467e276c -r 1fc845afa3ac bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Mon Mar 09 11:58:43 2015 -0400
+++ b/bowtie2_wrapper.xml	Tue Jul 21 13:00:51 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="0.4">
+<tool id="bowtie2" name="Bowtie2" version="0.5">
     <!-- Wrapper compatible with Bowtie version 2.2.4 -->
     <description>- map reads against reference genome</description>
     <version_command>bowtie2 --version</version_command>
@@ -145,18 +145,19 @@
         
         #elif str( $analysis_type.analysis_type_selector ) == "cline":
             ${analysis_type.cline}
-        #end if    
+        #end if
         
+        -S "galaxy_bowtie_2_output.sam" &amp;&amp;
+
         ## view/sort and output BAM file
-        | samtools view -Su - | samtools sort -o - - > $output
+        ( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output )
 
         ## rename unaligned sequence files
         #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
-            #set left  = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' )
-            #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' )
-        
-            ; mv $left $output_unaligned_reads_l;
-            mv $right $output_unaligned_reads_r
+            #from os.path import splitext
+            #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
+            &amp;&amp; mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
+            &amp;&amp; mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
         #end if
         
     </command>