Mercurial > repos > iuc > data_manager_selection_background

comparison data_manager/data_manager_selection_background.py @ 3:10ac95ec81d9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
author iuc
date Wed, 25 Aug 2021 21:07:59 +0000
parents e4f07770b340
children
comparison
equal deleted inserted replaced
2:e4f07770b340 3:10ac95ec81d9
109 parser.add_argument('--label', dest='label', action='store', required=True, help='Label to display') 109 parser.add_argument('--label', dest='label', action='store', required=True, help='Label to display')
110 parser.add_argument('--uri', dest='uri', action='store', help='URI for the sequences') 110 parser.add_argument('--uri', dest='uri', action='store', help='URI for the sequences')
111 parser.add_argument('--dataset', dest='dataset', action='store', help='Path for the sequences') 111 parser.add_argument('--dataset', dest='dataset', action='store', help='Path for the sequences')
112 112
113 args = parser.parse_args() 113 args = parser.parse_args()
114 114 dbkey = str(args.dbkey)
115 work_dir = os.getcwd()
116 115
117 if args.uri is not None: 116 if args.uri is not None:
118 background_fasta = url_download(args.uri) 117 background_fasta = url_download(args.uri)
119 else: 118 else:
120 background_fasta = args.dataset 119 background_fasta = args.dataset
121 120
122 table_entry = '%s.fa' % args.dbkey 121 with open(args.output) as fh:
123 shutil.copy(background_fasta, os.path.join(work_dir, table_entry)) 122 params = json.load(fh)
123 target_directory = params['output_data'][0]['extra_files_path']
124 os.makedirs(target_directory, exist_ok=True)
125 table_entry = '%s.fa' % dbkey
126 shutil.copy(background_fasta, os.path.join(target_directory, table_entry))
124 127
125 # Update Data Manager JSON and write to file 128 # Update Data Manager JSON and write to file
126 data_manager_entry = { 129 data_manager_entry = {
127 'data_tables': { 130 'data_tables': {
128 'selection_background': {'value': args.dbkey, 'label': args.label, 'path': table_entry} 131 'selection_background': {'value': dbkey, 'label': args.label, 'path': table_entry}
129 } 132 }
130 } 133 }
131 134
132 with open(os.path.join(args.output), 'w+') as fh: 135 with open(os.path.join(args.output), 'w+') as fh:
133 json.dump(data_manager_entry, fh, sort_keys=True) 136 json.dump(data_manager_entry, fh, sort_keys=True)