Mercurial > repos > dfornika > data_manager_build_kraken2_database

comparison data_manager/make_json.py @ 0:7e43f66abe9d draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
author dfornika
date Thu, 28 Feb 2019 02:32:38 -0500
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-1:000000000000 0:7e43f66abe9d
1 import argparse
2 import json
3 import os
4 import shutil
5
6
7 def main(args):
8 data_manager_entry = {}
9 data_manager_entry['value'] = args.database.lower()
10 data_manager_entry['name'] = args.database
11 data_manager_entry['path'] = '.'
12 data_manager_json = dict(data_tables=dict(kraken2_databases=data_manager_entry))
13 params = json.loads(open(args.output).read())
14 target_directory = params['output_data'][0]['extra_files_path']
15 os.mkdir(target_directory)
16 output_path = os.path.join(os.getcwd(), 'kraken2-database')
17 for filename in os.listdir(output_path):
18 shutil.move(os.path.join(output_path, filename), target_directory)
19 file(args.output, 'w').write(json.dumps(data_manager_json))
20
21
22 if __name__ == '__main__':
23 parser = argparse.ArgumentParser(description='Create data manager json.')
24 parser.add_argument('--db', dest='database', action='store', help='Database name')
25 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
26 args = parser.parse_args()
27 main(args)