Mercurial > repos > gga > apollo_fetch_jbrowse
changeset 9:d8bb1f9b85b2 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639
| author | gga |
|---|---|
| date | Mon, 29 Jul 2019 10:09:38 -0400 |
| parents | 331a3bde732e |
| children | dca2fb399ee6 |
| files | fetch_organism_jbrowse.xml json2iframe.py macros.xml |
| diffstat | 3 files changed, 10 insertions(+), 6 deletions(-) [+] |
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--- a/fetch_organism_jbrowse.xml Wed Apr 10 13:52:10 2019 -0400 +++ b/fetch_organism_jbrowse.xml Mon Jul 29 10:09:38 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.3" profile="16.04"> +<tool id="fetch_jbrowse" name="Retrieve JBrowse" version="@WRAPPER_VERSION@" profile="16.04"> <description>for an organism, from Apollo</description> <macros> <import>macros.xml</import> @@ -15,7 +15,7 @@ @ADMIN_AUTH@ @ORG_OR_GUESS@ -$jbrowse.files_path/ +$jbrowse.files_path/ "$__user_email__" &&
--- a/json2iframe.py Wed Apr 10 13:52:10 2019 -0400 +++ b/json2iframe.py Mon Jul 29 10:09:38 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 @@ <style type="text/css">body {{margin: 0;}} iframe {{border: 0;width: 100%;height: 100%}}</style> </head> <body> - <iframe src="{base_url}/annotator/loadLink?loc={chrom}&organism={orgId}&tracklist=1"></iframe> + <iframe src="{base_url}/annotator/loadLink?loc={chrom}&organism={orgId}{tracklist}"></iframe> </body> </html> """ - 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 ''))
--- a/macros.xml Wed Apr 10 13:52:10 2019 -0400 +++ b/macros.xml Mon Jul 29 10:09:38 2019 -0400 @@ -1,5 +1,7 @@ <?xml version="1.0"?> <macros> + <token name="@WRAPPER_VERSION@">4.0.0</token> + <xml name="requirements"> <requirements> <requirement type="package" version="2.7">python</requirement> @@ -99,6 +101,7 @@ <xml name="citations"> <citations> + <citation type="doi">10.1371/journal.pcbi.1006790</citation> </citations> </xml> <xml name="gff3_input"> @@ -123,7 +126,7 @@ **Citation** If you use this tool in Galaxy, please cite: -Eric Rasche (2016), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_ +Helena Rasche, Anthony Bretaudeau, and Mateo Boudet (2019), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_ ]]> </token> </macros>