Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 62:ab0d6782a95f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
author fubar
date Thu, 28 Mar 2024 04:51:06 +0000
parents 81d535970196
children c81902830900
comparison
equal deleted inserted replaced
61:e7a6f7a7148d 62:ab0d6782a95f
66 else: 66 else:
67 guseuri.append("no") 67 guseuri.append("no")
68 jc = jbC( 68 jc = jbC(
69 outdir=args.outdir, 69 outdir=args.outdir,
70 jbrowse2path=args.jbrowse2path, 70 jbrowse2path=args.jbrowse2path,
71 genomes=[ 71 )
72 genomes=[
72 { 73 {
73 "path": x, 74 "path": x,
74 "label": genome_names[i], 75 "label": genome_names[i],
75 "useuri": guseuri[i], 76 "useuri": guseuri[i],
76 "meta": { 77 "meta": {
78 "dataset_dname": genome_names[i], 79 "dataset_dname": genome_names[i],
79 }, 80 },
80 } 81 }
81 for i, x in enumerate(genome_paths) 82 for i, x in enumerate(genome_paths)
82 ], 83 ],
83 ) 84 logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
84 85 assref_name = jc.process_genomes(genomes[0])
85 jc.process_genomes()
86 default_session_data = { 86 default_session_data = {
87 "visibility": { 87 "visibility": {
88 "default_on": [], 88 "default_on": [],
89 "default_off": [], 89 "default_off": [],
90 }, 90 },
94 listtracks = trackList 94 listtracks = trackList
95 # foo.paf must have a foo_paf.fasta or fasta.gz to match 95 # foo.paf must have a foo_paf.fasta or fasta.gz to match
96 tnames = [x[2] for x in listtracks] 96 tnames = [x[2] for x in listtracks]
97 texts = [x[1] for x in listtracks] 97 texts = [x[1] for x in listtracks]
98 for i, track in enumerate(listtracks): 98 for i, track in enumerate(listtracks):
99 track_conf = {"trackfiles": [], "category": "autogenerated"} 99 track_conf = {"trackfiles": [], "category": "autogenerated", "assemblyNames": assref_name}
100 tpath, trext, trackname = track[:3] 100 tpath, trext, trackname = track[:3]
101 track_conf["dataset_id"] = trackname 101 track_conf["dataset_id"] = trackname
102 useuri = "no" 102 useuri = "no"
103 if tpath.startswith("http://") or tpath.startswith("https://"): 103 if tpath.startswith("http://") or tpath.startswith("https://"):
104 useuri = "yes" 104 useuri = "yes"