--- a/mitokmer.xml	Fri Apr 12 14:58:18 2019 -0400
+++ b/mitokmer.xml	Mon Apr 22 09:37:19 2019 -0400
@@ -29,16 +29,16 @@
 	#set $fwd = "R1.fasta"
 	#set $rev = "R2.fasta"
 	#end if
-	ln -s $forward $fwd;
-	ln -s $reverse $rev;
+	ln -s $forward $__tool_directory__/process/$fwd;
+	ln -s $reverse $__tool_directory__/process/$rev;
 	#if $reads.reads_select == "single"
 	#set $rev = "none"
 	#end if
-	mkdir ./output;
+	mkdir $__tool_directory__/output;
 	python $__tool_directory__/kmer_read_m3.py
-	-w $__tool_directory__
-	-d ./output
-	-i $fwd $rev
+	-w $__tool_directory__/
+	-d $__tool_directory__/output
+	-i $__tool_directory__/process/$fwd $__tool_directory__/process/$rev
 
     ]]></command>
     <inputs>