comparison bismark_wrapper.py @ 18:bb74e17e47d7 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 02087ce2966cf8b4aac9197a41171e7f986c11d1"

17:aa9bf0f29a9f

        cmd.append('--fastq')

    # alignment options
    if args.num_threads > 2:
        # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each
        cmd.extend(['-p', str(math.ceil(args.num_threads / 2))])
    if args.seed_mismatches:
        cmd.extend(['-N', str(args.seed_mismatches)])
    if args.seed_len:
        cmd.extend(['-L', str(args.seed_len)])
    if args.seed_extention_attempts:

18:bb74e17e47d7

        cmd.append('--fastq')

    # alignment options
    if args.num_threads > 2:
        # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each
        cmd.extend(['-p', str(int(math.floor(args.num_threads / 2)))])
    if args.seed_mismatches:
        cmd.extend(['-N', str(args.seed_mismatches)])
    if args.seed_len:
        cmd.extend(['-L', str(args.seed_len)])
    if args.seed_extention_attempts: