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
line wrap: on
line diff
--- 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()