diff macros.xml @ 4:3d6570bffdb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"

--- a/macros.xml	Mon Aug 07 17:29:19 2017 -0400
+++ b/macros.xml	Wed Dec 04 06:51:27 2019 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">1.2.3</token>
+    <token name="@WRAPPER_VERSION@">1.3.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
+            <requirement type="package" version="1.1.1">kraken</requirement>
         </requirements>
     </xml>
     <xml name="version_command">
@@ -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>