# HG changeset patch
# User dfornika
# Date 1557534895 14400
# Node ID b60b0a9523db91816fc6c3a4f85801f639ea97a6
# Parent  21cd25cc1ab21f6a89610a44a0f540960a8a91cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit c003994256543a5a4e99a1909135cce4f9b61692-dirty

diff -r 21cd25cc1ab2 -r b60b0a9523db data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Wed May 08 18:49:14 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Fri May 10 20:34:55 2019 -0400
@@ -124,6 +124,8 @@
         now + ")"
     ])
 
+    database_path = database_value
+
     # download the minikraken2 data
     src = urlopen(
         'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz'
@@ -133,7 +135,11 @@
         shutil.copyfileobj(src, dst)
     # unpack the downloaded archive to the target directory
     with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
-        fh.extractall(target_directory)
+        for member in fh.getmembers():
+            if member.isreg():
+                member.name = os.path.basename(member.name)
+                fh.extract(member, os.path.join(target_directory, database_path))
+
 
     data_table_entry = {
         'data_tables': {
@@ -141,7 +147,7 @@
                 {
                     "value": database_value,
                     "name": database_name,
-                    "path": database_value,
+                    "path": database_path,
                 }
             ]
         }
diff -r 21cd25cc1ab2 -r b60b0a9523db data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Wed May 08 18:49:14 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Fri May 10 20:34:55 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta">
+<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta">
     <macros>
         <xml name="common_params">
             <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />