comparison autogenJB2.py @ 39:bc57164eb270 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661

38:07849bf248e3

        "--pafreferencemeta",
        help="Repeatable. Each is a 'pafname,filepath,refname,filepath,refname....'. Every paf must have a corresponding one ",
        default=[],
        action="append",
    )

    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
    parser.add_argument("--outdir", help="Output directory", required=True)
    args = parser.parse_args()
    sessName = args.sessName
    # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
    trackList = [x.strip().split(",") for x in args.trackmeta if x > '']
    refList = [x.strip().split(",") for x in args.referencemeta if x > '']

                x[0] for x in listgenomes
            ]  # expect genome_1_genomename.fasta etc
            genome_names = [x[2] for x in listgenomes]
            jc = jbC(
                outdir=args.outdir,
                genomes=[
                    {
                        "path": x,
                        "meta": {
                            "name": genome_names[i],

39:bc57164eb270

        "--pafreferencemeta",
        help="Repeatable. Each is a 'pafname,filepath,refname,filepath,refname....'. Every paf must have a corresponding one ",
        default=[],
        action="append",
    )
    parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda")
    parser.add_argument("--outdir", help="Output directory", required=True)
    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
    args = parser.parse_args()
    sessName = args.sessName
    # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
    trackList = [x.strip().split(",") for x in args.trackmeta if x > '']
    refList = [x.strip().split(",") for x in args.referencemeta if x > '']

                x[0] for x in listgenomes
            ]  # expect genome_1_genomename.fasta etc
            genome_names = [x[2] for x in listgenomes]
            jc = jbC(
                outdir=args.outdir,
                jbrowse2path=args.jbrowse2path,
                genomes=[
                    {
                        "path": x,
                        "meta": {
                            "name": genome_names[i],