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(-) [+]
line wrap: on
line diff
--- 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>