# HG changeset patch # User gga # Date 1564409425 14400 # Node ID f26ac3b582e1b9ca759fccb091ffb66d5225db91 # Parent 2c749ed310daecb8432c4d82275836a62c37333d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639 diff -r 2c749ed310da -r f26ac3b582e1 json2iframe.py --- a/json2iframe.py Wed Apr 10 14:07:45 2019 -0400 +++ b/json2iframe.py Mon Jul 29 10:10:25 2019 -0400 @@ -10,10 +10,11 @@ parser.add_argument('apollo', help='Complete Apollo URL') parser.add_argument('json', type=argparse.FileType("r"), help='JSON Data') parser.add_argument('external_apollo_url') + parser.add_argument('--tracklist', action='store_true') args = parser.parse_args() - # https://fqdn/apollo/annotator/loadLink?loc=NC_005880:0..148317&organism=326&tracks= + # https://fqdn/apollo/annotator/loadLink?loc=NC_005880:0..148317&organism=326 data = json.load(args.json) # This is base64 encoded to get past the toolshed's filters. @@ -24,9 +25,9 @@ - + """ - print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data[0]['id'])) + print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data[0]['id'], tracklist='&tracklist=1' if args.tracklist else '')) diff -r 2c749ed310da -r f26ac3b582e1 list_organisms.xml --- a/list_organisms.xml Wed Apr 10 14:07:45 2019 -0400 +++ b/list_organisms.xml Mon Jul 29 10:10:25 2019 -0400 @@ -1,5 +1,5 @@ - + in Apollo macros.xml diff -r 2c749ed310da -r f26ac3b582e1 macros.xml --- a/macros.xml Wed Apr 10 14:07:45 2019 -0400 +++ b/macros.xml Mon Jul 29 10:10:25 2019 -0400 @@ -1,5 +1,7 @@ + 4.0.0 + python @@ -99,6 +101,7 @@ + 10.1371/journal.pcbi.1006790 @@ -123,7 +126,7 @@ **Citation** If you use this tool in Galaxy, please cite: -Eric Rasche (2016), `Galaxy Apollo Tools `_ +Helena Rasche, Anthony Bretaudeau, and Mateo Boudet (2019), `Galaxy Apollo Tools `_ ]]>