# HG changeset patch
# User thondeboer
# Date 1526422349 14400
# Node ID fc1c7b6fb7b67dc40c188b21f0bbc6292ae9dfb8
# Parent  5bcfac4f8116c3782532ed6e201b4f4d5163e3eb
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

diff -r 5bcfac4f8116 -r fc1c7b6fb7b6 computeGC.xml
--- a/computeGC.xml	Tue May 15 17:12:43 2018 -0400
+++ b/computeGC.xml	Tue May 15 18:12:29 2018 -0400
@@ -18,7 +18,7 @@
 		> out.genomecov
 	&& python2 $__tool_directory__/utilities/computeGC.py
 		#if $in_type.input_type == "built-in":
-		  -r ${in_type.reference.path}
+		  -r ${in_type.reference.fields.path}
 		#else:
 		  -r ${in_type.reference}
 		#end if
diff -r 5bcfac4f8116 -r fc1c7b6fb7b6 genMutModel.xml
--- a/genMutModel.xml	Tue May 15 17:12:43 2018 -0400
+++ b/genMutModel.xml	Tue May 15 18:12:29 2018 -0400
@@ -12,7 +12,7 @@
 	## Filenames and extensions are important, so make some links to make life easier downstream
 	ln -s $mutation_file mutation_file.vcf
 	#if $in_type.input_type == "built-in":
-	&& ln ${in_type.reference.fields.path} reference.fa
+	&& ln -s ${in_type.reference.fields.path} reference.fa
 	#else:
 	&& ln ${in_type.reference} reference.fa
 	#end if