Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 64:497fd2d27aa2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty
author fubar
date Thu, 28 Mar 2024 09:15:57 +0000
parents ac00dcfb5d1d
children c81902830900
comparison
equal deleted inserted replaced
63:ac00dcfb5d1d 64:497fd2d27aa2
1139 self.config_json["assemblies"].append(asstrack) 1139 self.config_json["assemblies"].append(asstrack)
1140 else: 1140 else:
1141 self.config_json["assemblies"] = [ 1141 self.config_json["assemblies"] = [
1142 asstrack, 1142 asstrack,
1143 ] 1143 ]
1144 url = "%s.paf" % (trackData["label"]) 1144 lab = trackData["label"]
1145 url = "%s.paf" % (lab)
1145 dest = "%s/%s" % (self.outdir, url) 1146 dest = "%s/%s" % (self.outdir, url)
1146 self.symlink_or_copy(os.path.realpath(data), dest) 1147 self.symlink_or_copy(os.path.realpath(data), dest)
1147 trackDict = { 1148 trackDict = {
1148 "type": "SyntenyTrack", 1149 "type": "SyntenyTrack",
1149 "trackId": tId, 1150 "trackId": tId,
1155 "adapter": { 1156 "adapter": {
1156 "type": "PAFAdapter", 1157 "type": "PAFAdapter",
1157 "pafLocation": {"uri": url}, 1158 "pafLocation": {"uri": url},
1158 "assemblyNames": passnames, 1159 "assemblyNames": passnames,
1159 }, 1160 },
1161 "displays": [
1162 {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
1163 {
1164 "type": "LinearComparativeDisplay",
1165 "displayId": "%s-LinearComparativeDisplay" % lab,
1166 },
1167 {
1168 "type": "LinearSyntenyDisplay",
1169 "displayId": "%s-LinearSyntenyDisplay" % lab,
1170 },
1171 {
1172 "type": "LGVSyntenyDisplay",
1173 "displayId": "%s-LGVSyntenyDisplay" % lab,
1174 },
1175 ],
1160 } 1176 }
1161 style_json = { 1177 style_json = {
1162 "displays": [ 1178 "displays": [
1163 { 1179 {
1164 "type": "LinearBasicDisplay", 1180 "type": "SyntenyDisplay",
1165 "displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"], 1181 "displayId": "%s-SyntenyDisplay" % lab,
1166 } 1182 }
1167 ] 1183 ]
1168 } 1184 }
1169 trackDict["style"] = style_json 1185 trackDict["style"] = style_json
1170 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) 1186 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)