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changeset 8:dc383ecbf839 draft

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Tue, 15 May 2018 23:09:17 -0400
parents fc1c7b6fb7b6
children 441103f02a11
files genMutModel.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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>