--- a/realigner_target_creator.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/realigner_target_creator.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,9 +1,10 @@
-<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.0">
+<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.1">
   <description>for use in local realignment</description>
-  <expand macro="requirements" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
@@ -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":
@@ -73,12 +75,12 @@
         </param>
       </when>
     </conditional>
-    
+
     <repeat name="rod_bind" title="Known Variants" help="Using data sets of known variants (-known,--known &amp;lt;known&amp;gt;)">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Variant Type">
             <option value="dbsnp" selected="True">dbSNP</option>
-            <option value="snps">SNPs</option>  
+            <option value="snps">SNPs</option>
             <option value="indels">INDELs</option>
             <option value="custom">Custom</option>
           </param>
@@ -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>
@@ -124,7 +130,7 @@
           <param name="mismatchFraction" value="0.15" />
           <param name="minReadsAtLocus" value="4" />
           <param name="maxIntervalSize" value="500" />
-          <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /> 
+          <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" />
           <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
       </test>
   </tests>