comparison jbrowse2.py @ 35:15da358c3108 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty

34:2893ef33fba9

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_hicab(self, data, trackData, hicOpts, **kwargs):
        rel_dest = os.path.join("data", trackData["label"] + ".hic")
        dest = os.path.join(self.outdir, rel_dest)

        self.symlink_or_copy(os.path.realpath(data), dest)

        self._add_track(
            trackData["label"],
            trackData["key"],
            trackData["category"],
            rel_dest,
            config={},
        )

    def add_sparql(self, url, query, query_refnames, trackData):

        json_track_data = {
            "type": "FeatureTrack",
            "trackId": id,
            "name": trackData["label"],
            "adapter": {
                "type": "SPARQLAdapter",
                "endpoint": {"uri": url, "locationType": "UriLocation"},
                "queryTemplate": query,
            },
            "category": [trackData["category"]],
            "assemblyNames": [self.genome_name],
        }

        if query_refnames:
            json_track_data["adapter"]["refNamesQueryTemplate"]: query_refnames

        self.subprocess_check_call(
            [
                "jbrowse",
                "add-track-json",
                "--target",
                os.path.join(self.outdir, "data"),
                json_track_data,
            ]
        )

        # Doesn't work as of 1.6.4, might work in the future
        # self.subprocess_check_call([
        #     'jbrowse', 'add-track',
        #     '--trackType', 'sparql',
        #     '--name', trackData['label'],
        #     '--category', trackData['category'],
        #     '--target', os.path.join(self.outdir, 'data'),
        #     '--trackId', id,
        #     '--config', '{"queryTemplate": "%s"}' % query,
        #     url])

    def process_annotations(self, track):
        category = track["category"].replace("__pd__date__pd__", TODAY)
        for i, (
            dataset_path,
            dataset_ext,

                self.add_bigwig(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext == "bam":
                real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][
                    "bam_index"
                ]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

                self.add_bam(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["pileup"],
                    bam_index=real_indexes[i],
                )
            elif dataset_ext == "cram":
                real_indexes = track["conf"]["options"]["cram"]["cram_indices"][
                    "cram_index"

                                x.attrib["ext"],
                                x.attrib["label"],
                                metadata,
                            )
                        )
        else:
            # For tracks without files (rest, sparql)
            track_conf["trackfiles"].append(
                (
                    "",  # N/A, no path for rest or sparql
                    track.attrib["format"],
                    track.find("options/label").text,
                    {},
                )
            )

        if is_multi_bigwig:
            metadata = metadata_from_node(x.find("metadata"))

            track_conf["trackfiles"].append(

35:15da358c3108

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def process_annotations(self, track):
        category = track["category"].replace("__pd__date__pd__", TODAY)
        for i, (
            dataset_path,
            dataset_ext,

                self.add_bigwig(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext == "bam":
                real_indexes = track["conf"]["options"]["bam"]["bam_indices"][
                    "bam_index"
                ]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

                self.add_bam(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["bam"],
                    bam_index=real_indexes[i],
                )
            elif dataset_ext == "cram":
                real_indexes = track["conf"]["options"]["cram"]["cram_indices"][
                    "cram_index"

                                x.attrib["ext"],
                                x.attrib["label"],
                                metadata,
                            )
                        )

        if is_multi_bigwig:
            metadata = metadata_from_node(x.find("metadata"))

            track_conf["trackfiles"].append(