comparison bismark_methylation_extractor.py @ 20:ff6ee551b153 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 2d8f9bfd501f1cd82b5cf0429c1b02b3784392ab"

19:359f8b60d316

    output_dir = tempfile.mkdtemp()
    cmd = ['bismark_methylation_extractor', '--no_header', '-o', output_dir]
    # Set up all options
    if args.multicore > 3:
        # divide multicore by 3 here since bismark will spawn ~3 jobs.
        cmd.extend(['--multicore', str(math.ceil(args.multicore / 3))])
    if args.single_end:
        cmd.append('--single-end')
    else:
        cmd.append('--paired-end')
    if args.no_overlap:

20:ff6ee551b153

    output_dir = tempfile.mkdtemp()
    cmd = ['bismark_methylation_extractor', '--no_header', '-o', output_dir]
    # Set up all options
    if args.multicore > 3:
        # divide multicore by 3 here since bismark will spawn ~3 jobs.
        cmd.extend(['--multicore', str(int(math.floor(args.multicore / 3)))])
    if args.single_end:
        cmd.append('--single-end')
    else:
        cmd.append('--paired-end')
    if args.no_overlap: