comparison autogenJB2.py @ 60:81d535970196 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a

59:f807e219cec3

                if keys:
                    for key in keys:
                        if trext in [
                            "bigwig",
                            "gff3",
                            "gff",
                            "vcf",
                            "maf",
                        ]:
                            default_session_data["visibility"]["default_on"].append(key)
                        else:
                            default_session_data["visibility"]["default_off"].append(
                                key
                            )
            # general_data = {
            # "analytics": root.find("metadata/general/analytics").text,
            # "primary_color": root.find("metadata/general/primary_color").text,
            # "secondary_color": root.find("metadata/general/secondary_color").text,
            # "tertiary_color": root.find("metadata/general/tertiary_color").text,

60:81d535970196

                if keys:
                    for key in keys:
                        if trext in [
                            "bigwig",
                            "gff", "gff3",
                            "vcf",
                            "maf",
                        ]:
                            default_session_data["visibility"]["default_on"].append(key)
                        else:
                            default_session_data["visibility"]["default_off"].append(
                                key
                            )
                        if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
                            ttype = "LinearBasicDisplay"
                            if trext == "vcf":
                                ttype = "LinearVariantDisplay"
                            style_json = {
                            "type": ttype,
                            "trackShowLabels": False,
                            "trackShowDescriptions": False
                            }
                            default_session_data["style"][key] = style_json
            # general_data = {
            # "analytics": root.find("metadata/general/analytics").text,
            # "primary_color": root.find("metadata/general/primary_color").text,
            # "secondary_color": root.find("metadata/general/secondary_color").text,
            # "tertiary_color": root.find("metadata/general/tertiary_color").text,