# HG changeset patch
# User devteam
# Date 1432068066 14400
# Node ID 656215d2a79331929f0ec6a1f02a72cc8ffbce04
# Parent  7d6b55e6417ed1aec1127890d1db445e2ce61145
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit cb1743eafd4ca98be0148d557770ef8635cc8d4c-dirty

diff -r 7d6b55e6417e -r 656215d2a793 kraken.xml
--- a/kraken.xml	Wed Apr 22 13:03:24 2015 -0400
+++ b/kraken.xml	Tue May 19 16:41:06 2015 -0400
@@ -8,6 +8,7 @@
     </macros>
     <command>
         <![CDATA[
+        @SET_DATABASE_PATH@ &&
         kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ 
         "$input_sequences"
         #if $split_reads:
diff -r 7d6b55e6417e -r 656215d2a793 macros.xml
--- a/macros.xml	Wed Apr 22 13:03:24 2015 -0400
+++ b/macros.xml	Tue May 19 16:41:06 2015 -0400
@@ -25,5 +25,6 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
-    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.path}/${kraken_database.fields.name}</token>
+    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
+    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
 </macros>
\ No newline at end of file
diff -r 7d6b55e6417e -r 656215d2a793 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 22 13:03:24 2015 -0400
+++ b/tool_dependencies.xml	Tue May 19 16:41:06 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="kraken" version="0.10.5">
-      <repository changeset_revision="c949a8bd92ec" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="e79fee8f87fa" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>