# HG changeset patch
# User dfornika
# Date 1551738102 18000
# Node ID a811afe91eabae9246bf02fbb3335b4079f259de
# Parent  d120504e741a1e6ea25bca390227b1dff66c502f
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty

diff -r d120504e741a -r a811afe91eab kraken2.xml
--- a/kraken2.xml	Mon Mar 04 17:17:43 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 17:21:42 2019 -0500
@@ -9,7 +9,7 @@
     <version_command>kraken2 --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
-        @SET_DATABASE_PATH@
+        @SET_DATABASE_PATH@ &&
         kraken2
             --threads \${GALAXY_SLOTS:-1}
 	    --db '$kraken2_database'
diff -r d120504e741a -r a811afe91eab macros.xml
--- a/macros.xml	Mon Mar 04 17:17:43 2019 -0500
+++ b/macros.xml	Mon Mar 04 17:21:42 2019 -0500
@@ -15,4 +15,5 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
+    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken2_database.fields.path}/${kraken2_database.fields.name}' ]; then export KRAKEN2_DB_PATH='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN2_DB_PATH='${kraken_database.fields.path}'; fi</token>
 </macros>