comparison idr_download_by_ids.py @ 7:f067504aa92a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"

6:5c743356df83

def download_image_data(
    image_ids,
    channel=None, z_stack=0, frame=0,
    coord=(0, 0), width=0, height=0, region_spec='rectangle',
    skip_failed=False, download_tar=False
):
    # basic argument sanity checks and adjustments
    prefix = 'image-'
    # normalize image ids by stripping off prefix if it exists
    image_ids = [

    if region_spec not in ['rectangle', 'center']:
        raise ValueError(
            'Got unknown value "{0}" as region_spec argument'
            .format(region_spec)
        )

    with ExitStack() as exit_stack:
        # connect to idr
        conn = exit_stack.enter_context(
            BlitzGateway(
                'public', 'public',
                host='idr.openmicroscopy.org',
                secure=True
            )
        )
        # exit_stack.callback(conn.connect().close)
        if download_tar:
            # create an archive file to write images to

        '--skip-failed', action='store_true'
    )
    p.add_argument(
        '--download-tar', action='store_true'
    )
    args = p.parse_args()
    if not args.image_ids:
        args.image_ids = sys.stdin.read().split()
    if 'center' in args:
        args.coord, args.width, args.height = (

7:f067504aa92a

def download_image_data(
    image_ids,
    channel=None, z_stack=0, frame=0,
    coord=(0, 0), width=0, height=0, region_spec='rectangle',
    skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=True, omero_username='public', omero_password='public'
):
    # basic argument sanity checks and adjustments
    prefix = 'image-'
    # normalize image ids by stripping off prefix if it exists
    image_ids = [

    if region_spec not in ['rectangle', 'center']:
        raise ValueError(
            'Got unknown value "{0}" as region_spec argument'
            .format(region_spec)
        )
    with ExitStack() as exit_stack:
        conn = exit_stack.enter_context(
            BlitzGateway(
                omero_username, omero_password,
                host=omero_host,
                secure=omero_secured
            )
        )
        # exit_stack.callback(conn.connect().close)
        if download_tar:
            # create an archive file to write images to

        '--skip-failed', action='store_true'
    )
    p.add_argument(
        '--download-tar', action='store_true'
    )
    p.add_argument(
        '-oh', '--omero-host', type=str, default="idr.openmicroscopy.org"
    )
    p.add_argument(
        '--omero-secured', action='store_false'
    )
    p.add_argument(
        '-u', '--omero-username', type=str, default="public"
    )
    p.add_argument(
        '-p', '--omero-password', type=str, default="public"
    )
    args = p.parse_args()
    if not args.image_ids:
        args.image_ids = sys.stdin.read().split()
    if 'center' in args:
        args.coord, args.width, args.height = (