--- a/unified_genotyper.xml	Wed Feb 19 04:39:38 2014 -0500
+++ b/unified_genotyper.xml	Mon Aug 25 17:43:11 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.7">
+<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.0">
   <description>SNP and indel caller</description>
   <expand macro="requirements" />
   <macros>
@@ -72,7 +72,6 @@
                 --excludeAnnotation "${annotation}"
             #end for
         #end if
-        ${analysis_param_type.multiallelic}
         #if str( $analysis_param_type.sample_ploidy ) != '':
           --sample_ploidy "$analysis_param_type.sample_ploidy"
         #end if
@@ -199,7 +198,7 @@
             <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
           </options>
         </param>
-        <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
+        <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" />
     </expand>
   </inputs>
   <outputs>
@@ -294,4 +293,5 @@
 
 @CITATION_SECTION@
   </help>
+  <expand macro="citations" />
 </tool>