Mercurial > repos > bgruening > pileometh

changeset 6:f6beeefdba25 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 033c712216994524fdd120b771052ac4ca9e51c0-dirty
author bgruening
date Fri, 18 Sep 2015 10:39:46 -0400
parents 89a6b89777a0
children e17c14e33075
files PileOMeth.xml
diffstat 1 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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":