--- a/realigner_target_creator.xml	Tue Mar 11 07:42:09 2014 -0400
+++ b/realigner_target_creator.xml	Wed Feb 18 11:36:59 2015 -0500
@@ -1,6 +1,7 @@
-<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.7">
+<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.1">
   <description>for use in local realignment</description>
   <expand macro="requirements" />
+  <expand macro="version_command" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
@@ -37,7 +38,8 @@
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
     #end for
-   
+
+    $allow_n_cigar_reads
     #include source=$standard_gatk_options#
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
@@ -97,13 +99,17 @@
           </when>
         </conditional>
     </repeat>
-    
+
+    <expand macro="allow_n_cigar_reads" />
     <expand macro="gatk_param_type_conditional" />
-    
+
     <expand macro="analysis_type_conditional">
-        <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
-        <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
-        <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
+        <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" 
+            help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
+        <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" 
+            help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
+        <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" 
+            help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
         <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
     </expand>
   </inputs>
@@ -164,4 +170,5 @@
 
 @CITATION_SECTION@
   </help>
+  <expand macro="citations" />
 </tool>