Mercurial > repos > fubar > jbrowse2

changeset 52:ae12977c0e5e draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
author fubar
date Thu, 07 Mar 2024 06:41:01 +0000
parents e18f2d6c4dbe
children bdfa6a7c4543
files autogenJB2.py
diffstat 1 files changed, 5 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- 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: