# HG changeset patch
# User dcorreia
# Date 1477414084 14400
# Node ID 7f2fdaeaa7238b7f047b131b40bfe6e61cb8eb5a
# Parent  b0d5f7b87402b88bc5c9812cb6b7e826b483dbb6
Uploaded

diff -r b0d5f7b87402 -r 7f2fdaeaa723 phyml.xml
--- a/phyml.xml	Wed Oct 19 13:16:07 2016 -0400
+++ b/phyml.xml	Tue Oct 25 12:48:04 2016 -0400
@@ -11,11 +11,14 @@
                source="stdrr"
                level="fatal"/>
     </stdio>
-
-    <command><![CDATA[
+    <command>
+        <![CDATA[
           ##PhyML outputs are based on input path and we need to create outputs in working_dir.
           ln -sf $input '${input.name}';
-         
+          #if ($usetree.inputTree == "true"):
+          ln -sf ${$usetree.userInputTree} ${$usetree.userInputTree.name};
+          #end if
+
           phyml --input '${input.name}'
                 ${phylip_format}
                 --datatype ${seq.type_of_seq}
@@ -45,17 +48,16 @@
                 -o ${optimisationTopology}
                 
                 #if ($usetree.inputTree == "true"):
-                    --inputtree ${inputTree.userInputTree}
+                    --inputtree ${$usetree.userInputTree.name}
                 #end if
                 
                 #if ($numStartSeed != "0"):
                     --r_seed ${numStartSeed}
                 #end if
                 
-                --no_memory_check
-                --quiet > ${output_stdout};
+                --no_memory_check > ${output_stdout};
                 grep 'failed' ${output_stdout} >&2;
-            ]]>
+        ]]>
     </command>
     <inputs>
         <param name="input" type="data" format="phylip, phy" label="Alignment file" help="phylip format"/>