Mercurial > repos > thondeboer > neat_genreads

diff genMutModel.xml @ 9:441103f02a11 draft

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Wed, 16 May 2018 02:05:26 -0400
parents dc383ecbf839
children 7d10b55965c9
line wrap: on
line diff
--- a/genMutModel.xml	Tue May 15 23:09:17 2018 -0400
+++ b/genMutModel.xml	Wed May 16 02:05:26 2018 -0400
@@ -10,13 +10,13 @@
   <command detect_errors="exit_code">
     <![CDATA[
 	## Filenames and extensions are important, so make some links to make life easier downstream
-	ln -s $mutation_file mutation_file.vcf
+	ln -s $mutation_file mutation_file.vcf;
 	#if $in_type.input_type == "built-in":
-	&& ln -s ${in_type.reference.fields.path} reference.fa
+	ln -s ${in_type.reference.fields.path} reference.fa;
 	#else:
-	&& ln -s ${in_type.reference} reference.fa
+	ln -s ${in_type.reference} reference.fa;
 	#end if
-    && python2 $__tool_directory__/utilities/genMutModel.py
+    python2 $__tool_directory__/utilities/genMutModel.py
 		-r reference.fa
 		-m mutation_file.vcf
 		-o $genMutModel_modelfile