comparison jbrowse2.py @ 121:478ee3e780de draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a6f013087aa66546a843298e2584604668f9e140

120:af482048ca1a

    def text_index(self):
        # Index tracks
        args = [
            "jbrowse",
            "text-index",
            "--target",
            self.outdir,
            "--assemblies",
            self.genome_name,
        ]

        tracks = ",".join(self.trackIdlist)
        if tracks:
            args += ["--tracks", tracks]

            self.subprocess_check_call(args)

    def add_hic(self, data, trackData):
        """
        HiC adapter.
        https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md

    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version=JB2VER)
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()
    removeMe = string.punctuation.replace('.','').replace('/','').replace('-','')
    nopunct = str.maketrans(dict.fromkeys(removeMe))
    # This should be done ASAP
    GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
    # Sometimes this comes as `localhost` without a protocol
    if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):

        )
    )
    jc.write_config()
    # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
    # jc.add_defsess_to_index(default_session_data)
    # jc.text_index() not sure what broke here.

121:478ee3e780de

    def text_index(self):
        # Index tracks
        args = [
            "jbrowse",
            "text-index"
        ]
        self.subprocess_check_call(args)

    def add_hic(self, data, trackData):
        """
        HiC adapter.
        https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md

    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version=JB2VER)
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()
    removeMe = string.punctuation.replace('.', ' ').replace('/', '').replace('-', '')
    # first is a space because space needs to be added here for removal from labels as paths.
    nopunct = str.maketrans(dict.fromkeys(removeMe))
    # This should be done ASAP
    GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
    # Sometimes this comes as `localhost` without a protocol
    if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):

        )
    )
    jc.write_config()
    # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
    # jc.add_defsess_to_index(default_session_data)
    # this command line tool appears currently broken - or at least not working here.
    # jc.text_index()