diff macros.xml @ 8:8ba2174315aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f

--- a/macros.xml	Thu Sep 13 09:44:31 2018 -0400
+++ b/macros.xml	Mon Jan 14 16:48:56 2019 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">1.2.4</token>
+    <token name="@WRAPPER_VERSION@">1.3.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
@@ -23,6 +23,10 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
-    <token name="@INPUT_DATABASE@">--db '${kraken_database.fields.name}'</token>
-    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH='${kraken_database.fields.path}'</token>
+    <!-- See the kraken_databases.loc.sample documentation,
+	 this if statement is for backward compatibility as early
+	 versions of the wrapper assumed the UI facing field name
+	 was also part of the directory path -->
+    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
+    <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
 </macros>