# HG changeset patch
# User bgruening
# Date 1442587186 14400
# Node ID f6beeefdba255a69b4cc2e50bd6db81b4d06fda8
# Parent  89a6b89777a05d9ae6632c605927e302652db895
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 033c712216994524fdd120b771052ac4ca9e51c0-dirty

diff -r 89a6b89777a0 -r f6beeefdba25 PileOMeth.xml
--- a/PileOMeth.xml	Fri Sep 18 10:24:54 2015 -0400
+++ b/PileOMeth.xml	Fri Sep 18 10:39:46 2015 -0400
@@ -11,8 +11,10 @@
         <regex match="Error:" />
         <regex match="Exception:" />
     </stdio>
-    <version_command>PileOMeth --version</version_command>
+    <version_command><![CDATA[PileOMeth 2>&1  | head -n 2 | tail -n 1]]></version_command>
     <command><![CDATA[
+        ln -s $reference_source.ref_file reference.fasta &&
+
         PileOMeth
             $main_task.task
 
@@ -34,7 +36,8 @@
                 $advanced_options.CHH
             #end if
 
-            $reference_source.ref_file
+            reference.fasta
+
             $input_sortedAlignBAM
 
             #if $main_task.task == "mbias":