# HG changeset patch
# User dfornika
# Date 1522347133 14400
# Node ID 8be8c9f08008bad2d620038c68b72d3be981dfcf
# Parent 385d86a69684329452ed7b3f9cdd1802204cec59
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/mentalist_v0.2 commit 5ff26fad09082423f1ddc9cf408dad04d36558cf-dirty
diff -r 385d86a69684 -r 8be8c9f08008 data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml Sat Mar 24 23:22:30 2018 -0400
+++ b/data_managers/data_manager_conf.xml Thu Mar 29 14:12:13 2018 -0400
@@ -60,4 +60,21 @@
+
diff -r 385d86a69684 -r 8be8c9f08008 data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.py Thu Mar 29 14:12:13 2018 -0400
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import json
+import os
+import shutil
+
+
+def main(args):
+ data_manager_entry = {}
+ data_manager_entry['value'] = args.database.lower()
+ data_manager_entry['name'] = args.database
+ data_manager_entry['path'] = '.'
+ data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
+ params = json.loads(open(args.output).read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ output_path = os.path.join(os.getcwd(), 'kraken-database')
+ for filename in os.listdir(output_path):
+ shutil.move(os.path.join(output_path, filename), target_directory)
+ file(args.output, 'w').write(json.dumps(data_manager_json))
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description='Create data manager json.')
+ parser.add_argument('--db', dest='database', action='store', help='Database name')
+ parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+ args = parser.parse_args()
+ main(args)
diff -r 385d86a69684 -r 8be8c9f08008 data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_remove_db/data_manager/mentalist_remove_db.xml Thu Mar 29 14:12:13 2018 -0400
@@ -0,0 +1,26 @@
+
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+ mentalist
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+ 10.1101/172858
+ 10.1099/mgen.0.000146
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+
diff -r 385d86a69684 -r 8be8c9f08008 data_managers/data_manager_mentalist_remove_db/tool-data/mentalist_databases.loc.sample
diff -r 385d86a69684 -r 8be8c9f08008 data_managers/data_manager_mentalist_remove_db/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_remove_db/tool_data_table_conf.xml.sample Thu Mar 29 14:12:13 2018 -0400
@@ -0,0 +1,8 @@
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