# HG changeset patch
# User dcorreia
# Date 1476882409 14400
# Node ID a1375fb40c035b49db1ac2c7130ddf2ab9b212b1
# Parent  b89b7278dff5067230982d308215b9a5b419ceea
Uploaded

diff -r b89b7278dff5 -r a1375fb40c03 phyml.xml
--- a/phyml.xml	Mon Jul 04 10:33:59 2016 -0400
+++ b/phyml.xml	Wed Oct 19 09:06:49 2016 -0400
@@ -14,9 +14,9 @@
 
     <command><![CDATA[
           ##PhyML outputs are based on input path and we need to create outputs in working_dir.
-          ln -sf $input input_tmp;
+          ln -sf $input '${input.name}';
          
-          phyml --input input_tmp
+          phyml --input '${input.name}'
                 ${phylip_format}
                 --datatype ${seq.type_of_seq}
                 --multiple ${nb_data_set}