comparison bismark_methylation_extractor.py @ 4:427fb56f2e41 draft default tip

- new options - fixes

3:7eefe5d6eecd

def __main__():
    #Parse Command Line
    parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')

    # input options
    parser.add_argument( '--infile', help='Input file in SAM format.' )
    parser.add_argument( '--single-end', dest='single_end', action="store_true" )
    parser.add_argument( '--paired-end', dest='paired_end', action="store_true" )

    parser.add_argument( '--report-file', dest='report_file' )

    # Build methylation extractor command
    output_dir = tempfile.mkdtemp()
    cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'

    additional_opts = ''
    # Set up all options
    if args.single_end:
        additional_opts += ' --single-end '

4:427fb56f2e41

def __main__():
    #Parse Command Line
    parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')

    # input options
    parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )

    parser.add_argument( '--infile', help='Input file in SAM format.' )
    parser.add_argument( '--single-end', dest='single_end', action="store_true" )
    parser.add_argument( '--paired-end', dest='paired_end', action="store_true" )

    parser.add_argument( '--report-file', dest='report_file' )

    # Build methylation extractor command
    output_dir = tempfile.mkdtemp()
    cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'
    if args.bismark_path:
        # add the path to the bismark perl scripts, that is needed for galaxy
        cmd = os.path.join(args.bismark_path, cmd)

    additional_opts = ''
    # Set up all options
    if args.single_end:
        additional_opts += ' --single-end '