comparison data_manager/novocraft_index_builder.py @ 6:8dd4b25716d1 draft

planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 05004076adb510abc08f6c1e28ba22b2c1a29534

5:b7c01f1d6451

log = logging.getLogger(__name__)

from json import loads, dumps

DEFAULT_DATA_TABLE_NAME = "novocraft_indexes"

def get_dbkey_id_name(params, dbkey_description=None):
    dbkey = params['param_dict']['dbkey']
    # TODO: ensure sequence_id is unique and does not already appear in location file
    sequence_id = params['param_dict']['sequence_id']

def main():
    parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this")
    parser.add_argument('output_filename')
    parser.add_argument('--dbkey_description')
    parser.add_argument('--data_table_name', default='novocraft_indexes')
    args = parser.parse_args()

    filename = args.output_filename

    params = loads(open(filename).read())

6:8dd4b25716d1

log = logging.getLogger(__name__)

from json import loads, dumps

DEFAULT_DATA_TABLE_NAME = "novocraft_index"

def get_dbkey_id_name(params, dbkey_description=None):
    dbkey = params['param_dict']['dbkey']
    # TODO: ensure sequence_id is unique and does not already appear in location file
    sequence_id = params['param_dict']['sequence_id']

def main():
    parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this")
    parser.add_argument('output_filename')
    parser.add_argument('--dbkey_description')
    parser.add_argument('--data_table_name', default='novocraft_index')
    args = parser.parse_args()

    filename = args.output_filename

    params = loads(open(filename).read())