Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 47:3e53204c2419 draft

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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)