--- a/bwa.xml	Fri Jan 08 17:02:09 2016 -0500
+++ b/bwa.xml	Tue Jan 19 11:20:59 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="0.7.12">
+<tool id="bwa" name="Map with BWA" version="@VERSION@.1">
   <description>- map short reads (&lt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
@@ -69,28 +69,7 @@
   <expand macro="stdio" />
   <command>
 <![CDATA[
-    #set $reference_fasta_filename = "localref.fa"
-
-    #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
-
-        ## The following shell commands decide which of the BWA indexing algorithms (IS or BWTSW) will be run
-        ## depending on the size of the input FASTA dataset
-        ( size=`stat -c %s "${reference_source.ref_file}" 2>/dev/null`; ## Linux
-          if [ $? -ne 0 ]; then
-              size=\$(stat -f %z "${reference_source.ref_file}"); ## OSX
-          fi &&
-          if [ "\$size" -lt 2000000000 ]; then
-              echo "Reference genome size is \$size bytes, generating BWA index with is algorithm";
-              bwa index -a is "${reference_fasta_filename}";
-          else
-              echo "Reference genome size is \$size bytes, generating BWA index with bwtsw algorithm";
-              bwa index -a bwtsw "${reference_fasta_filename}";
-          fi
-        ) &&
-    #else:
-        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
-    #end if
+    @set_reference_fasta_filename@
 
     ## setup vars for rg handling...
     @define_read_group_helpers@
@@ -246,25 +225,7 @@
   </command>
 
   <inputs>
-    
-    <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
-        <option value="cached">Use a built-in genome index</option>
-        <option value="history">Use a genome from history and build index</option>
-      </param>
-      <when value="cached">
-        <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
-          <options from_data_table="bwa_mem_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
-      </when>
-    </conditional>
+    <expand macro="reference_source_conditional" />
     <conditional name="input_type">
       <param name="input_type_selector" type="select" label="Select input type" help="Select between fastq and bam datasets and between paired and single end data">
         <option value="paired">Paired fastq</option>