comparison jbrowse2.py @ 9:a26c41e304c3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b

8:9a168aa68f06

    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, genomes):
        self.usejson = True
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_paths = genomes
        self.genome_name = None

                    }
                },
            },
            "displays": [
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        style_json = self._prepare_track_style(trackDict)

            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
    x = open(args.xml, "r").read()
    jc.config_json["tracks"] = jc.tracksToAdd
    if jc.usejson:
        jc.write_config()
    jc.add_default_session(default_session_data)

    # jc.text_index() not sure what broke here.

9:a26c41e304c3

    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, genomes):
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_paths = genomes
        self.genome_name = None

                    }
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        style_json = self._prepare_track_style(trackDict)

            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
    x = open(args.xml, "r").read()
    jc.config_json["tracks"] = jc.tracksToAdd
    jc.write_config()
    jc.add_default_session(default_session_data)

    # jc.text_index() not sure what broke here.