# HG changeset patch
# User cropgeeks
# Date 1510746164 18000
# Node ID 8a06f49972d0919fb954146613377a0fc6ade600
# Parent  6777844fd6386c5422c4c21b00eff316c6c844b0
Added more optional parameters to mabcstats.xml and pedverf1stats.xml

diff -r 6777844fd638 -r 8a06f49972d0 lib/flapjack.jar
Binary file lib/flapjack.jar has changed
diff -r 6777844fd638 -r 8a06f49972d0 mabcstats.xml
--- a/mabcstats.xml	Tue Nov 14 11:28:35 2017 -0500
+++ b/mabcstats.xml	Wed Nov 15 06:42:44 2017 -0500
@@ -9,6 +9,9 @@
 		-m $map
 		-g $genotypes
 		-q $qtls
+		#if $traits
+			-t $traits
+		#end if
 		-r $parent1
 		-d $parent2
 		-model $model
@@ -40,6 +43,11 @@
 			label="Flapjack QTL file"
 			help="Flapjack-formatted (tab-delimited text) input file of QTL data."/>
 
+		<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 recurrent parent"
 			help="The index of the recurrent parent in the genotype file."/>
diff -r 6777844fd638 -r 8a06f49972d0 pedverf1stats.xml
--- 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"/>