Mercurial > repos > gga > apollo_create_or_update

changeset 15:1e28978d7136 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f742b16e6e4c33b9abdb633405298e05760c84b"
author gga
date Tue, 08 Jun 2021 09:16:29 +0000
parents 4abaab60f9e1
children 9e7b8c7185ad
files json2iframe.py macros.xml test-data/create_org/output.json test-data/create_org/output2.json
diffstat 4 files changed, 13 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/json2iframe.py	Wed Aug 19 06:58:44 2020 -0400
+++ b/json2iframe.py	Tue Jun 08 09:16:29 2021 +0000
@@ -22,7 +22,7 @@
         <html>
             <head>
                 <title>Embedded Apollo Access</title>
-                <style type="text/css">body {{margin: 0;}} iframe {{border: 0;width: 100%;height: 100%}}</style>
+                <style type="text/css">body {{margin: 0;}} iframe {{border: 0;width: 100%;height: 100vh}}</style>
             </head>
             <body>
                 <iframe src="{base_url}/annotator/loadLink?loc={chrom}&organism={orgId}{tracklist}"></iframe>
@@ -30,4 +30,7 @@
         </html>
     """
 
-    print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data[0]['id'], tracklist='&tracklist=1' if args.tracklist else ''))
+    if isinstance(data, list):
+        print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data[0]['id'], tracklist='&tracklist=1' if args.tracklist else ''))
+    else:
+        print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data['id'], tracklist='&tracklist=1' if args.tracklist else ''))
--- a/macros.xml	Wed Aug 19 06:58:44 2020 -0400
+++ b/macros.xml	Tue Jun 08 09:16:29 2021 +0000
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@WRAPPER_VERSION@">4.2.5</token>
+  <token name="@WRAPPER_VERSION@">4.2.13</token>
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="4.2.5">apollo</requirement>
+      <requirement type="package" version="4.2.13">apollo</requirement>
       <yield/>
     </requirements>
   </xml>
--- a/test-data/create_org/output.json	Wed Aug 19 06:58:44 2020 -0400
+++ b/test-data/create_org/output.json	Tue Jun 08 09:16:29 2021 +0000
@@ -9,8 +9,10 @@
   "directory": "/XX/apollo_shared_dir/1",
   "publicMode": false,
   "valid": true,
+  "genomeFastaIndex": "seq/genome.fasta.fai",
   "genus": "genus",
   "species": null,
   "id": "xx",
-  "nonDefaultTranslationTable": null
+  "nonDefaultTranslationTable": null,
+  "genomeFasta": "seq/genome.fasta"
 }
--- a/test-data/create_org/output2.json	Wed Aug 19 06:58:44 2020 -0400
+++ b/test-data/create_org/output2.json	Tue Jun 08 09:16:29 2021 +0000
@@ -9,8 +9,10 @@
   "directory": "/XX/apollo_shared_dir/3",
   "publicMode": false,
   "valid": true,
+  "genomeFastaIndex": "seq/genome.fasta.fai",
   "genus": "genus2",
   "species": "sp",
   "id": "xx",
-  "nonDefaultTranslationTable": null
+  "nonDefaultTranslationTable": null,
+  "genomeFasta": "seq/genome.fasta"
 }