def seal(reference, forward_in, output_file, reverse_in='NA', returncmd=False, **kwargs):
    """
    Runs seal from the bbtools package.
    :param reference: Reference file, in fasta format.
    :param returncmd: If set to true, function will return the cmd string passed to subprocess as a third value.
    :param forward_in: Forward reads, fastq format.
    :param output_file: Output file to put rpkm statistics into.
    :param reverse_in: Reverse reads. Not necessary to specify if in same folder and follow _R1/_R2 convention.
    :param kwargs: Arguments to give to seal in parameter=argument format. See seal documentation for full list.
    :return: out and err: stdout string and stderr string from running seal.
    """
    options = kwargs_to_string(kwargs)
    if os.path.isfile(forward_in.replace('_R1', '_R2')) and reverse_in == 'NA' and '_R1' in forward_in:
        reverse_in = forward_in.replace('_R1', '_R2')
        cmd = 'seal.sh ref={} in={} in2={} rpkm={} nodisk{}'.format(reference, forward_in, reverse_in, output_file, options)
    elif reverse_in == 'NA':
        cmd = 'seal.sh ref={} in={} rpkm={} nodisk{}'.format(reference, forward_in, output_file, options)
    else:
        cmd = 'seal.sh ref={} in={} in2={} rpkm={} nodisk{}'.format(reference, forward_in, reverse_in, output_file, options)
    out, err = accessoryfunctions.run_subprocess(cmd)
    if returncmd:
        return out, err, cmd
    else:
        return out, err
Runs seal from the bbtools package.
    :param reference: Reference file, in fasta format.
    :param returncmd: If set to true, function will return the cmd string passed to subprocess as a third value.
    :param forward_in: Forward reads, fastq format.
    :param output_file: Output file to put rpkm statistics into.
    :param reverse_in: Reverse reads. Not necessary to specify if in same folder and follow _R1/_R2 convention.
    :param kwargs: Arguments to give to seal in parameter=argument format. See seal documentation for full list.
    :return: out and err: stdout string and stderr string from running seal.