Mercurial > repos > iuc > idr_download_by_ids
diff 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"
author | iuc |
---|---|
date | Thu, 05 Nov 2020 23:29:40 +0000 |
parents | 5c743356df83 |
children | 97f70f7ed077 |
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--- a/idr_download_by_ids.py Mon Jul 06 19:33:59 2020 -0400 +++ b/idr_download_by_ids.py Thu Nov 05 23:29:40 2020 +0000 @@ -112,7 +112,7 @@ 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 + 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-' @@ -127,14 +127,12 @@ '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 + omero_username, omero_password, + host=omero_host, + secure=omero_secured ) ) # exit_stack.callback(conn.connect().close) @@ -356,6 +354,18 @@ 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()