Mercurial > repos > devteam > data_manager_build_kraken_database
diff data_manager/make_json.py @ 0:c3276afba416 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Thu, 23 Jul 2015 10:54:53 -0400 (2015-07-23) |
parents | |
children | 065d8a4d74f4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/make_json.py Thu Jul 23 10:54:53 2015 -0400 @@ -0,0 +1,28 @@ +import json +import argparse +import os +import shutil + +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() + +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__': + main(args) +