comparison jbrowse2.py @ 54:d6b0feb22584 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c

53:bdfa6a7c4543

                gname = gname.split()[0]
                passnames.append(gname)
                # trouble from spacey names in command lines avoidance
                if gname not in self.genome_names:
                    # ignore if already there - eg for duplicates among pafs.
                    asstrack = self.make_assembly(pgpaths[i], gname)
                    self.genome_names.append(gname)
                    if self.config_json.get("assemblies", None):
                        self.config_json["assemblies"].append(asstrack)
                    else:
                        self.config_json["assemblies"] = [

54:d6b0feb22584

                gname = gname.split()[0]
                passnames.append(gname)
                # trouble from spacey names in command lines avoidance
                if gname not in self.genome_names:
                    # ignore if already there - eg for duplicates among pafs.
                    useuri = pgpaths[i].startswith('http://') or pgpaths[i].startswith('https://')
                    asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                    self.genome_names.append(gname)
                    if self.config_json.get("assemblies", None):
                        self.config_json["assemblies"].append(asstrack)
                    else:
                        self.config_json["assemblies"] = [