Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 37:7adde511daa1 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Thu, 29 Feb 2024 00:51:45 +0000
parents 15da358c3108
children 07849bf248e3
comparison
equal deleted inserted replaced
36:5f39f745682f 37:7adde511daa1
1135 self.add_bigwig( 1135 self.add_bigwig(
1136 dataset_path, 1136 dataset_path,
1137 outputTrackConfig, 1137 outputTrackConfig,
1138 ) 1138 )
1139 elif dataset_ext == "bam": 1139 elif dataset_ext == "bam":
1140 real_indexes = track["conf"]["options"]["bam"]["bam_indices"][ 1140 real_indexes = track["conf"]["options"]["bam"]["bam_index"]
1141 "bam_index"
1142 ]
1143 if not isinstance(real_indexes, list): 1141 if not isinstance(real_indexes, list):
1144 real_indexes = [real_indexes] 1142 real_indexes = [real_indexes]
1145 1143
1146 self.add_bam( 1144 self.add_bam(
1147 dataset_path, 1145 dataset_path,
1148 outputTrackConfig, 1146 outputTrackConfig,
1149 track["conf"]["options"]["bam"], 1147 track["conf"]["options"]["bam"],
1150 bam_index=real_indexes[i], 1148 bam_index=real_indexes[i],
1151 ) 1149 )
1152 elif dataset_ext == "cram": 1150 elif dataset_ext == "cram":
1153 real_indexes = track["conf"]["options"]["cram"]["cram_indices"][ 1151 real_indexes = track["conf"]["options"]["cram"]["cram_index"][
1154 "cram_index" 1152 "cram_index"
1155 ] 1153 ]
1156 if not isinstance(real_indexes, list): 1154 if not isinstance(real_indexes, list):
1157 real_indexes = [real_indexes] 1155 real_indexes = [real_indexes]
1158 1156