Mercurial > repos > dfornika > data_manager_build_kraken2_database
view data_manager/make_json.py @ 0:7e43f66abe9d draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
author | dfornika |
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date | Thu, 28 Feb 2019 02:32:38 -0500 |
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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(kraken2_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(), 'kraken2-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)