--- a/haplotype_caller.xml	Wed Feb 19 04:39:38 2014 -0500
+++ b/haplotype_caller.xml	Mon Aug 25 17:43:11 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.7">
+<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.0">
   <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description>
   <expand macro="requirements" />
   <macros>
@@ -158,7 +158,7 @@
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk2_annotations">
             <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+            <filter type="static_value" value="HaplotypeCaller" column="tools_valid_for"/>
           </options>
         </param>
         <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
@@ -191,7 +191,7 @@
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk2_annotations">
             <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+            <filter type="static_value" value="HaplotypeCaller" column="tools_valid_for"/>
           </options>
         </param>
 
@@ -320,4 +320,5 @@
 
 @CITATION_SECTION@
   </help>
+  <expand macro="citations" />
 </tool>