comparison data_manager/vsnp_genbank_fetcher.py @ 1:98babcb65125 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_genbank commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

0:efed56c325da

def download(dbkey, name, url, out_file):

    with open(out_file) as fh:
        params = json.loads(fh.read())

    workdir = params['output_data'][0]['extra_files_path']
    os.makedirs(workdir)
    file_path = url_download(url, workdir)
    entry_name = os.path.basename(file_path)

    data_manager_entry['path'] = file_path
    data_manager_entry['description'] = "Genbank file for %s" % name
    data_manager_json["data_tables"]["vsnp_genbank"] = data_manager_entry

    with open(out_file, 'w') as fh:
        fh.write(json.dumps(data_manager_json, sort_keys=True))


parser = argparse.ArgumentParser()

parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey')

1:98babcb65125

def download(dbkey, name, url, out_file):

    with open(out_file) as fh:
        params = json.load(fh)

    workdir = params['output_data'][0]['extra_files_path']
    os.makedirs(workdir)
    file_path = url_download(url, workdir)
    entry_name = os.path.basename(file_path)

    data_manager_entry['path'] = file_path
    data_manager_entry['description'] = "Genbank file for %s" % name
    data_manager_json["data_tables"]["vsnp_genbank"] = data_manager_entry

    with open(out_file, 'w') as fh:
        json.dump(data_manager_json, fh, sort_keys=True)


parser = argparse.ArgumentParser()

parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey')