Mercurial > repos > devteam > data_manager_build_kraken_database

comparison data_manager/make_json.py @ 5:0a9ff888a4e2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
author iuc
date Tue, 18 Aug 2020 11:36:13 -0400
parents 065d8a4d74f4
children 889a857303e0
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4:6d7aef331be9 5:0a9ff888a4e2
14 target_directory = params['output_data'][0]['extra_files_path'] 14 target_directory = params['output_data'][0]['extra_files_path']
15 os.mkdir(target_directory) 15 os.mkdir(target_directory)
16 output_path = os.path.join(os.getcwd(), 'kraken-database') 16 output_path = os.path.join(os.getcwd(), 'kraken-database')
17 for filename in os.listdir(output_path): 17 for filename in os.listdir(output_path):
18 shutil.move(os.path.join(output_path, filename), target_directory) 18 shutil.move(os.path.join(output_path, filename), target_directory)
19 file(args.output, 'w').write(json.dumps(data_manager_json)) 19 with open(args.output, 'w') as out:
20 out.write(json.dumps(data_manager_json, sort_keys=True))
20 21
21 22
22 if __name__ == '__main__': 23 if __name__ == '__main__':
23 parser = argparse.ArgumentParser(description='Create data manager json.') 24 parser = argparse.ArgumentParser(description='Create data manager json.')
24 parser.add_argument('--db', dest='database', action='store', help='Database name') 25 parser.add_argument('--db', dest='database', action='store', help='Database name')