Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.py @ 47:3e53204c2419 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
| author | fubar |
|---|---|
| date | Wed, 06 Mar 2024 00:23:02 +0000 |
| parents | 4181e97c70a7 |
| children | 460d5b6c5d98 |
comparison
equal
deleted
inserted
replaced
| 46:4181e97c70a7 | 47:3e53204c2419 |
|---|---|
| 1084 pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] | 1084 pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] |
| 1085 passnames = [self.genome_name] # always first | 1085 passnames = [self.genome_name] # always first |
| 1086 for i, gname in enumerate(pgnames): | 1086 for i, gname in enumerate(pgnames): |
| 1087 if len(gname.split()) > 1: | 1087 if len(gname.split()) > 1: |
| 1088 gname = gname.split()[0] | 1088 gname = gname.split()[0] |
| 1089 passnames.append(gname) | |
| 1089 # trouble from spacey names in command lines avoidance | 1090 # trouble from spacey names in command lines avoidance |
| 1090 if gname not in self.genome_names: | 1091 if gname not in self.genome_names: |
| 1091 passnames.append(gname) | |
| 1092 # ignore if already there - eg for duplicates among pafs. | 1092 # ignore if already there - eg for duplicates among pafs. |
| 1093 asstrack = self.make_assembly(pgpaths[i], gname) | 1093 asstrack = self.make_assembly(pgpaths[i], gname) |
| 1094 self.genome_names.append(gname) | 1094 self.genome_names.append(gname) |
| 1095 if self.config_json.get("assemblies", None): | 1095 if self.config_json.get("assemblies", None): |
| 1096 self.config_json["assemblies"].append(asstrack) | 1096 self.config_json["assemblies"].append(asstrack) |