--- a/bwa.xml	Fri Dec 18 18:51:08 2015 -0500
+++ b/bwa.xml	Fri Dec 30 08:10:56 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="0.4.2">
+<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>
@@ -68,41 +68,8 @@
   <expand macro="requirements" />
   <expand macro="stdio" />
   <command>
-    #set $reference_fasta_filename = "localref.fa"
-
-    #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
-
-        ## The following shell commands decide with of the BWA indexing algorithms (IS or BWTSW) will be run
-        ## depending ob the size of the input FASTA dataset
-           (
-            size=`stat -c %s "${reference_fasta_filename}" 2&gt;/dev/null`;                  ## Linux
-            if [ $? -eq 0 ];
-            then
-              if [ "\$size" -lt 2000000000 ];
-              then
-                bwa index -a is "${reference_fasta_filename}";
-              else
-                bwa index -a bwtsw "${reference_fasta_filename}";
-              fi;
-            fi;
-
-            eval \$(stat -s "${reference_fasta_filename}" 2&gt;/dev/null);                   ## OSX
-            if [ -n "\$st_size" ];
-            then
-              if [ "\$st_size" -lt 2000000000 ];
-              then
-                bwa index -a is "${reference_fasta_filename}";
-                echo "Generating BWA index with is algorithm";
-              else
-                bwa index -a bwtsw "${reference_fasta_filename}";
-                echo "Generating BWA index with bwtsw algorithm";
-              fi;
-            fi;
-            ) &amp;&amp;
-    #else:
-        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
-    #end if
+<![CDATA[
+    @set_reference_fasta_filename@
 
     ## setup vars for rg handling...
     @define_read_group_helpers@
@@ -134,7 +101,7 @@
         "${input_type.fastq_input1}"
       #end if
 
-      > first.sai &amp;&amp;
+      > first.sai &&
 
       bwa aln
       -t "\${GALAXY_SLOTS:-1}"
@@ -149,7 +116,7 @@
         "${input_type.fastq_input2}"
       #end if
 
-      > second.sai &amp;&amp;
+      > second.sai &&
 
       bwa sampe
 
@@ -178,7 +145,7 @@
 
       "${reference_fasta_filename}"
       "${input_type.fastq_input1}"
-      > first.sai &amp;&amp;
+      > first.sai &&
 
       bwa samse
 
@@ -202,7 +169,7 @@
 
       "${reference_fasta_filename}"
       "${input_type.bam_input}"
-      > first.sai &amp;&amp;
+      > first.sai &&
 
       bwa aln
       -t "\${GALAXY_SLOTS:-1}"
@@ -211,7 +178,7 @@
       @command_options@
       "${reference_fasta_filename}"
       "${input_type.bam_input}"
-      > second.sai &amp;&amp;
+      > second.sai &&
 
       bwa sampe
 
@@ -238,7 +205,7 @@
 
       "${reference_fasta_filename}"
       "${input_type.bam_input}"
-      > first.sai &amp;&amp;
+      > first.sai &&
 
       bwa samse
 
@@ -251,31 +218,12 @@
       "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
     #end if
 
-    | samtools view -Sb - > temporary_bam_file.bam &amp;&amp;
-
-    samtools sort -f temporary_bam_file.bam ${bam_output}
+    | samtools sort -O bam -o '$bam_output'
+]]>
   </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>