--- a/freebayes.xml	Fri Oct 09 15:47:24 2015 -0400
+++ b/freebayes.xml	Fri Oct 09 17:20:08 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="freebayes" name="FreeBayes" version="0.4">
+<tool id="freebayes" name="FreeBayes" version="0.4.1">
   <requirements>
     <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
@@ -80,7 +80,9 @@
     #elif str( $options_type.options_type_selector ) == "full":
  
         #if $options_type.optional_inputs.optional_inputs_selector:
-        
+       
+	  ${options_type.optional_inputs.report_monomorphic}
+ 
           #if $options_type.optional_inputs.output_trace_option:
             --trace "${output_trace}"
           #end if
@@ -122,7 +124,6 @@
         
 ## REPORTING
 
-        ${options_type.optional_inputs.report_monomorphic}
 
         #if str( $options_type.reporting.reporting_selector ) == "True":
             --pvar ${options_type.reporting.pvar}