# HG changeset patch
# User dfornika
# Date 1551748926 18000
# Node ID 269ea4b78bbb7422a61a39915a6af6fd0eb8b1a4
# Parent  da1a2d98dab18cf9ec1ef1b095b11cd91ff9dde8
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty

diff -r da1a2d98dab1 -r 269ea4b78bbb kraken2.xml
--- a/kraken2.xml	Mon Mar 04 17:29:41 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 20:22:06 2019 -0500
@@ -9,10 +9,9 @@
     <version_command>kraken2 --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
-        @SET_DATABASE_PATH@ &&
         kraken2
             --threads \${GALAXY_SLOTS:-1}
-	    --db '$kraken2_database'
+	    --db '${kraken2_database.fields.path}'
             #if $single_paired.single_paired_selector == 'yes'
                 '${single_paired.forward_input}' '${single_paired.reverse_input}'
             #elif $single_paired.single_paired_selector == "collection":
diff -r da1a2d98dab1 -r 269ea4b78bbb macros.xml
--- a/macros.xml	Mon Mar 04 17:29:41 2019 -0500
+++ b/macros.xml	Mon Mar 04 20:22:06 2019 -0500
@@ -15,5 +15,4 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
-    <token name="@SET_DATABASE_PATH@">export KRAKEN2_DB_PATH='${kraken2_database.fields.path}'</token>
 </macros>