Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.py @ 30:8f02a84ee278 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
| author | fubar |
|---|---|
| date | Wed, 21 Feb 2024 02:57:30 +0000 |
| parents | f728cf0df71d |
| children | cb4b32ca9968 |
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| 29:f728cf0df71d | 30:8f02a84ee278 |
|---|---|
| 1117 extra_metadata, | 1117 extra_metadata, |
| 1118 ) in enumerate(track["trackfiles"]): | 1118 ) in enumerate(track["trackfiles"]): |
| 1119 # Unsanitize labels (element_identifiers are always sanitized by Galaxy) | 1119 # Unsanitize labels (element_identifiers are always sanitized by Galaxy) |
| 1120 for key, value in mapped_chars.items(): | 1120 for key, value in mapped_chars.items(): |
| 1121 track_human_label = track_human_label.replace(value, key) | 1121 track_human_label = track_human_label.replace(value, key) |
| 1122 track_human_label = track_human_label.replace(" ","_") | |
| 1122 outputTrackConfig = { | 1123 outputTrackConfig = { |
| 1123 "category": category, | 1124 "category": category, |
| 1124 "style": {}, | 1125 "style": {}, |
| 1125 } | 1126 } |
| 1126 | 1127 |
| 1139 self.add_gff( | 1140 self.add_gff( |
| 1140 dataset_path, | 1141 dataset_path, |
| 1141 dataset_ext, | 1142 dataset_ext, |
| 1142 outputTrackConfig, | 1143 outputTrackConfig, |
| 1143 ) | 1144 ) |
| 1144 elif dataset_ext in ("hic",): | 1145 elif dataset_ext in ("hic","juicebox_hic"): |
| 1145 self.add_hic( | 1146 self.add_hic( |
| 1146 dataset_path, | 1147 dataset_path, |
| 1147 outputTrackConfig, | 1148 outputTrackConfig, |
| 1148 ) | 1149 ) |
| 1149 elif dataset_ext in ("cool", "mcool", "scool"): | 1150 elif dataset_ext in ("cool", "mcool", "scool"): |
| 1150 hic_url = "%s_%d.hic" % (track_human_label, i) | 1151 hic_url = "%s_%d.juicebox_hic" % (track_human_label, i) |
| 1151 hic_path = os.path.join(self.outdir, hic_url) | 1152 hic_path = os.path.join(self.outdir, hic_url) |
| 1152 self.subprocess_check_call( | 1153 self.subprocess_check_call( |
| 1153 [ | 1154 [ |
| 1154 "hictk", | 1155 "hictk", |
| 1155 "convert", | 1156 "convert", |