# HG changeset patch
# User dfornika
# Date 1557355754 14400
# Node ID 21cd25cc1ab21f6a89610a44a0f540960a8a91cd
# Parent  86bc169b0aeb15b181a41facbff7af842162e545
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 1137710d16538da15bcd87e1ba382e2afc00031f-dirty

diff -r 86bc169b0aeb -r 21cd25cc1ab2 data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Wed May 08 18:39:03 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Wed May 08 18:49:14 2019 -0400
@@ -267,7 +267,7 @@
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--extra-files-path', dest='extra_files_path', help='')
+    parser.add_argument('data_manager_json')
     parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
     parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
     parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
@@ -281,7 +281,7 @@
 
     data_manager_input = json.loads(open(args.data_manager_json).read())
 
-    target_directory = args.extra_files_path
+    target_directory = data_manager_input['output_data'][0]['extra_files_path']
 
     try:
         os.mkdir( target_directory )
diff -r 86bc169b0aeb -r 21cd25cc1ab2 data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Wed May 08 18:39:03 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Wed May 08 18:49:14 2019 -0400
@@ -15,7 +15,7 @@
     <command detect_errors="exit_code">
     <![CDATA[
         python '$__tool_directory__/kraken2_build_database.py'
-          --extra-files-path '$out_file.extra_files_path'
+          '${out_file}'
           --database-type ${database_type.database_type}
           #if $database_type.database_type == "minikraken"
             --minikraken2-version ${database_type.minikraken2_version}