Have Bowtie2 wrapper produce BAM rather than SAM output.

tools/sr_mapping/bowtie2_wrapper.py

@@ -65,7 +65,7 @@ def __main__():
         index_path = options.index_path
 
     # Build bowtie command.
-    cmd = 'bowtie2 %s -x %s %s -S %s'
+    cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s'
     
     # Set up reads.
     if options.single_paired == 'paired':

tools/sr_mapping/bowtie2_wrapper.xml

@@ -112,7 +112,7 @@
     </inputs>
 
     <outputs>
-        <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+        <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
           <actions>
             <conditional name="refGenomeSource.genomeSource">
               <when value="indexed">