comparison snippy_core_wrapper.py @ 9:caed59c13f82 draft

planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty

8:c441153cb4c2

from shutil import copyfile

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
    parser.add_argument('-i', '--indirs')
    args = parser.parse_args()

    snippy_core_command_line = ['snippy-core', '--ref', args.ref]

    for indir in args.indirs.split():
        base_name = os.path.basename(indir)
        sys.stderr.write(indir + '\n')
        copyfile(indir, base_name)
        sys.stderr.write('\n'.join([indir, base_name]) + '\n')
        subprocess.run(['tar', '-xf', base_name])

9:caed59c13f82

from shutil import copyfile

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
    parser.add_argument('-i', '--indirs' help='Comma-separated list of input datasets')
    args = parser.parse_args()

    snippy_core_command_line = ['snippy-core', '--ref', args.ref]

    for indir in args.indirs.split(','):
        base_name = os.path.basename(indir)
        sys.stderr.write(indir + '\n')
        copyfile(indir, base_name)
        sys.stderr.write('\n'.join([indir, base_name]) + '\n')
        subprocess.run(['tar', '-xf', base_name])