# HG changeset patch
# User thondeboer
# Date 1526440157 14400
# Node ID dc383ecbf839fc152b8fa1e3ec37fc8b5b745e6b
# Parent  fc1c7b6fb7b67dc40c188b21f0bbc6292ae9dfb8
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

diff -r fc1c7b6fb7b6 -r dc383ecbf839 genMutModel.xml
--- a/genMutModel.xml	Tue May 15 18:12:29 2018 -0400
+++ b/genMutModel.xml	Tue May 15 23:09:17 2018 -0400
@@ -14,7 +14,7 @@
 	#if $in_type.input_type == "built-in":
 	&& ln -s ${in_type.reference.fields.path} reference.fa
 	#else:
-	&& ln ${in_type.reference} reference.fa
+	&& ln -s ${in_type.reference} reference.fa
 	#end if
     && python2 $__tool_directory__/utilities/genMutModel.py
 		-r reference.fa
@@ -115,14 +115,14 @@
   <outputs>
 	<data format="txt"
 		  name="genMutModel_modelfile"
-		  label="${os.path.splitext($mutation_file.name)}_genMutModel.p"
+		  label="${os.path.splitext(str($mutation_file.name))[0]}_genMutModel.p"
 		  metadata_source="in_type.reference">
 	</data>
 	
 	<data format="simple"
 	      name="trinuc_file"
 		  from_work_dir="reference.fa.trinucCounts"
-	      label="${os.path.splitext($mutation_file.name)}_trinucCounts.tsv"
+	      label="${os.path.splitext(str($mutation_file.name))[0]}_trinucCounts.tsv"
 	      metadata_source="in_type.reference">
 		  <filter>misc['save_trinuc']</filter>
 	</data>