# HG changeset patch
# User cropgeeks
# Date 1493641844 14400
# Node ID 4ba88eb0e03b35d92a1f9e0a51f512d2894f21d6
# Parent  6fd2203fc221f82149c3870a697dafcaf8e421d0
Uploaded

diff -r 6fd2203fc221 -r 4ba88eb0e03b lib/commons-cli-1.4.jar
Binary file lib/commons-cli-1.4.jar has changed
diff -r 6fd2203fc221 -r 4ba88eb0e03b lib/flapjack.jar
Binary file lib/flapjack.jar has changed
diff -r 6fd2203fc221 -r 4ba88eb0e03b mabcstats.xml
--- a/mabcstats.xml	Thu Mar 09 09:24:42 2017 -0500
+++ b/mabcstats.xml	Mon May 01 08:30:44 2017 -0400
@@ -8,19 +8,19 @@
     -Xmx$advanced_options.memory
   #end if
   -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
-  -map=$map
-  -genotypes=$genotypes
-  -qtls=$qtls
-  -parent1=$parent1
-  -parent2=$parent2
-  -model=$model
-  -coverage=$coverage
+  -m $map
+  -g $genotypes
+  -q $qtls
+  -r $parent1
+  -d $parent2
+  -model $model
+  -coverage $coverage
   #if $advanced_options.show_advanced
     $advanced_options.decimalEnglish
   #end if
-  #if $create_project
-  -output=$output
-	-project=$project
+  -o $output
+  #if $create_project  
+    -p $project
   #end if	
   ]]></command>
 
@@ -47,7 +47,7 @@
 			truevalue="show" falsevalue="">
 		</param>
 		<when value="show">
-			<param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
+			<param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="True"
             label="Force English-style decimal marks"
             help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/>
 			<param name="memory" type="select" label="Memory"