comparison jbrowse2.py @ 30:8f02a84ee278 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919

29:f728cf0df71d

            extra_metadata,
        ) in enumerate(track["trackfiles"]):
            # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
            for key, value in mapped_chars.items():
                track_human_label = track_human_label.replace(value, key)
            outputTrackConfig = {
                "category": category,
                "style": {},
            }

                self.add_gff(
                    dataset_path,
                    dataset_ext,
                    outputTrackConfig,
                )
            elif dataset_ext in ("hic",):
                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):
                hic_url = "%s_%d.hic" % (track_human_label, i)
                hic_path = os.path.join(self.outdir, hic_url)
                self.subprocess_check_call(
                    [
                        "hictk",
                        "convert",

30:8f02a84ee278

            extra_metadata,
        ) in enumerate(track["trackfiles"]):
            # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
            for key, value in mapped_chars.items():
                track_human_label = track_human_label.replace(value, key)
            track_human_label = track_human_label.replace(" ","_")
            outputTrackConfig = {
                "category": category,
                "style": {},
            }

                self.add_gff(
                    dataset_path,
                    dataset_ext,
                    outputTrackConfig,
                )
            elif dataset_ext in ("hic","juicebox_hic"):
                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):
                hic_url = "%s_%d.juicebox_hic" % (track_human_label, i)
                hic_path = os.path.join(self.outdir, hic_url)
                self.subprocess_check_call(
                    [
                        "hictk",
                        "convert",