Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 39:bc57164eb270 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
author fubar
date Fri, 01 Mar 2024 01:03:09 +0000
parents 07849bf248e3
children 4181e97c70a7
comparison
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38:07849bf248e3 39:bc57164eb270
41 "--pafreferencemeta", 41 "--pafreferencemeta",
42 help="Repeatable. Each is a 'pafname,filepath,refname,filepath,refname....'. Every paf must have a corresponding one ", 42 help="Repeatable. Each is a 'pafname,filepath,refname,filepath,refname....'. Every paf must have a corresponding one ",
43 default=[], 43 default=[],
44 action="append", 44 action="append",
45 ) 45 )
46 46 parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda")
47 parser.add_argument("--outdir", help="Output directory", required=True)
47 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2") 48 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
48 parser.add_argument("--outdir", help="Output directory", required=True)
49 args = parser.parse_args() 49 args = parser.parse_args()
50 sessName = args.sessName 50 sessName = args.sessName
51 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key' 51 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
52 trackList = [x.strip().split(",") for x in args.trackmeta if x > ''] 52 trackList = [x.strip().split(",") for x in args.trackmeta if x > '']
53 refList = [x.strip().split(",") for x in args.referencemeta if x > ''] 53 refList = [x.strip().split(",") for x in args.referencemeta if x > '']
61 x[0] for x in listgenomes 61 x[0] for x in listgenomes
62 ] # expect genome_1_genomename.fasta etc 62 ] # expect genome_1_genomename.fasta etc
63 genome_names = [x[2] for x in listgenomes] 63 genome_names = [x[2] for x in listgenomes]
64 jc = jbC( 64 jc = jbC(
65 outdir=args.outdir, 65 outdir=args.outdir,
66 jbrowse2path=args.jbrowse2path,
66 genomes=[ 67 genomes=[
67 { 68 {
68 "path": x, 69 "path": x,
69 "meta": { 70 "meta": {
70 "name": genome_names[i], 71 "name": genome_names[i],