comparison data_manager/salmon_index_builder.py @ 3:6437fc47878f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 5f199df1a4ce3c569c3778e3eb67019fc1b0c8db"

2:57274fe5e01a

    return sequence_id, sequence_name


def build_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name):
    data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
    target_directory = params['output_data' ][0]['extra_files_path']
    if not os.path.exists(target_directory):
        os.mkdir(target_directory)
    args = ['salmon', 'index']
    if options.kmer_size != '':
        args.append('-k')

3:6437fc47878f

    return sequence_id, sequence_name


def build_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name):
    data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
    target_directory = params['output_data'][0]['extra_files_path']
    if not os.path.exists(target_directory):
        os.mkdir(target_directory)
    args = ['salmon', 'index']
    if options.kmer_size != '':
        args.append('-k')