Mercurial > repos > gga > apollo_create_or_update

changeset 9:29ce13734a5c draft

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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 10:09:54 -0400
parents 496444ad9291
children d72192ec8e39
files create_or_update_organism.xml json2iframe.py macros.xml
diffstat 3 files changed, 9 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/create_or_update_organism.xml	Wed Apr 10 14:00:29 2019 -0400
+++ b/create_or_update_organism.xml	Mon Jul 29 10:09:54 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="create_or_update" name="Create or Update Organism" version="3.4">
+<tool id="create_or_update" name="Create or Update Organism" version="@WRAPPER_VERSION@">
   <description>will create the organism if it doesn't exist, and update otherwise</description>
   <macros>
     <import>macros.xml</import>
--- a/json2iframe.py	Wed Apr 10 14:00:29 2019 -0400
+++ b/json2iframe.py	Mon Jul 29 10:09:54 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 14:00:29 2019 -0400
+++ b/macros.xml	Mon Jul 29 10:09:54 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>