--- a/bwa-mem.xml	Thu Jun 01 11:38:47 2017 -0400
+++ b/bwa-mem.xml	Sat Sep 30 13:37:06 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0">
   <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
@@ -63,6 +63,7 @@
         ${analysis_type.io_options.V}
         ${analysis_type.io_options.Y}
         ${analysis_type.io_options.M}
+        ${analysis_type.io_options.five}
       #end if
 
     #end if
@@ -226,6 +227,7 @@
             <option value="do_not_set" selected="True">Do not set</option>
           </param>
           <when value="set">
+            <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
             <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
             <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
             <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>