--- a/indel_realigner.xml	Tue Mar 11 07:42:09 2014 -0400
+++ b/indel_realigner.xml	Wed Feb 18 11:36:59 2015 -0500
@@ -1,6 +1,7 @@
-<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.7">
+<tool id="gatk2_indel_realigner" name="Indel Realigner" version="@VERSION@.1">
   <description>- perform local realignment</description>
   <expand macro="requirements" />
+  <expand macro="version_command" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
@@ -38,7 +39,8 @@
         #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
     -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
@@ -110,7 +112,8 @@
     </repeat>
     <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
     <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/>
-    
+
+    <expand macro="allow_n_cigar_reads" />
     <expand macro="gatk_param_type_conditional" />
     
     <expand macro="analysis_type_conditional">
@@ -206,4 +209,5 @@
 
 @CITATION_SECTION@
   </help>
+  <expand macro="citations" />
 </tool>