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changeset 56:8a06f49972d0 draft

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Added more optional parameters to mabcstats.xml and pedverf1stats.xml
author cropgeeks
date Wed, 15 Nov 2017 06:42:44 -0500
parents 6777844fd638
children 98b179705a21
files lib/flapjack.jar mabcstats.xml pedverf1stats.xml
diffstat 3 files changed, 24 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file lib/flapjack.jar has changed
--- 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."/>
--- 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"/>