# HG changeset patch
# User fubar
# Date 1709793661 0
# Node ID ae12977c0e5e50d54a4633bcf8e8f41ae820a77a
# Parent  e18f2d6c4dbef9b485f317c5f95b5e71ee6846c5
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty

diff -r e18f2d6c4dbe -r ae12977c0e5e autogenJB2.py
--- a/autogenJB2.py	Thu Mar 07 04:52:28 2024 +0000
+++ b/autogenJB2.py	Thu Mar 07 06:41:01 2024 +0000
@@ -90,14 +90,17 @@
                 "style": {},
                 "style_labels": {},
             }
-            track_conf = {}
             listtracks = trackList
             # foo.paf must have a foo_paf.fasta or fasta.gz to match
             tnames = [x[2] for x in listtracks]
             texts = [x[1] for x in listtracks]
             for i, track in enumerate(listtracks):
+                track_conf = {"trackfiles": [], "category": "autogenerated"}
                 tpath, trext, trackname = track[:3]
                 track_conf["dataset_id"] = trackname
+                useuri = "no"
+                if tpath.startswith('http://') or tpath.startswith('https://'):
+                    useuri = "yes"
                 if trext == "paf":
                     refname = trackname + "_paf.fasta"
                     refdat = [x[2] for x in listtracks if x[2] == refname]
@@ -136,14 +139,7 @@
                 track_conf["format"] = trext
                 track_conf["name"] = trackname
                 track_conf["label"] = trackname
-                useu = tpath.startswith('http://') or tpath.startswith('https://')
-                useuri = 'no'
-                if useu:
-                    useuri = 'yes'
-                    track_conf["trackfiles"] = [
-                        (tpath, trext, useuri, trackname, {}),
-                    ]
-                track_conf["category"] = "Autogenerated"
+                track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {}))
                 keys = jc.process_annotations(track_conf)
 
                 if keys: