comparison jbrowse2.py @ 37:7adde511daa1 draft

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

36:5f39f745682f

                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"
                ]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

37:7adde511daa1

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