# HG changeset patch
# User cropgeeks
# Date 1519232905 18000
# Node ID 805b78c41bac490af6872bc8fe29e88eeeff22ba
# Parent  dc02f001fd09278160f2c875cedabdac0e63b54f
Uploaded

diff -r dc02f001fd09 -r 805b78c41bac splitbysample.xml
--- a/splitbysample.xml	Wed Feb 21 12:03:38 2018 -0500
+++ b/splitbysample.xml	Wed Feb 21 12:08:25 2018 -0500
@@ -1,24 +1,20 @@
-<tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
+<tool id="flapjack_split_by_sample" name="Flapjack Split By Sample" version="0.0.1">
     <description>create a Flapjack project file from Flapjack formatted input files.</description>
-    <command><![CDATA[
+    <command>
         python $__tool_directory__/FlapjackProject.py
         -j $__tool_directory__/lib/flapjack.jar
-        -g $genotypes
-        -s $traits
+        -g '$genotypes'
+        -s '$traits'
         #if $map
-            -m $map
-        #end if
-        #if $name
-            -n $name
+            -m '$map'
         #end if
         #if $qtls
-            -q $qtls
+            -q '$qtls'
         #end if
         #if $adv_opts.show_advanced
             -M "$adv_opts.missingData"
             -S "$adv_opts.hetSep"
         #end if
-    ]]>
     </command>
     <inputs>
         <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"