# HG changeset patch
# User dfornika
# Date 1558638616 14400
# Node ID 7d384656966e0ee12df11548d250e92dadecc5fc
# Parent  40ea0695a0a0b2341b17eda76e2b8945266b4bcf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 616f23916e8c71295e1456d6df585c351bd64f86-dirty

diff -r 40ea0695a0a0 -r 7d384656966e data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Thu May 23 14:16:37 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Thu May 23 15:10:16 2019 -0400
@@ -227,7 +227,7 @@
     ]
 
     if kraken2_args['skip_maps']:
-        args += '--skip-maps'
+        args.append('--skip-maps')
 
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
@@ -256,7 +256,7 @@
         '--db', custom_database_name
     ]
 
-    subprocess.check_call(['kraken2-build'] + args, target_directory)
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     data_table_entry = {
         'data_tables': {
diff -r 40ea0695a0a0 -r 7d384656966e data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Thu May 23 14:16:37 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Thu May 23 15:10:16 2019 -0400
@@ -78,6 +78,15 @@
     <outputs>
         <data name="out_file" format="data_manager_json" />
     </outputs>
+    <tests>
+        <test>
+            <param name="database_type" value="custom" />
+            <param name="custom_fasta" value="adapter.fa" />
+            <param name="custom_database_name" value="database" />
+            <param name="skip_maps" value="true" />
+            <output name="out_file" value="kraken2_custom_data_manager.json" />
+        </test>
+    </tests>
     <help>
     </help>
     <citations>
diff -r 40ea0695a0a0 -r 7d384656966e test-data/kraken2_custom_data_manager.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken2_custom_data_manager.json	Thu May 23 15:10:16 2019 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"kraken2_databases": [{"path": "database", "name": "database", "value": "database"}]}}