--- a/pedverf1stats.xml	Tue Nov 14 11:28:35 2017 -0500
+++ b/pedverf1stats.xml	Wed Nov 15 06:42:44 2017 -0500
@@ -8,6 +8,12 @@
 		-cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats
 		-m $map
 		-g $genotypes
+		#if $qtls
+			-q $qtls
+		#end if
+		#if $traits
+			-t $traits
+		#end if
 		-f $parent1
 		-s $parent2
 		-o $output
@@ -33,6 +39,16 @@
 		<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
 			help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
 
+		<param format="fjqtl" name="qtls" type="data"
+			   label="Flapjack QTL file"
+			   help="Flapjack-formatted (tab-delimited text) input file of QTL data."
+			   optional="true"/>
+
+		<param format="fjphenotype" name="traits" type="data"
+			   label="Flapjack Trait file"
+			   help="Flapjack-formatted (tab-delimited text) input file of trait data."
+			   optional="true"/>
+
 		<param name="parent1" type="integer" value="1" label="Index of parent 1"
 			help="The index of the first parent in the genotype file"/>