Mercurial > repos > fubar > jbrowse2
changeset 68:c4eb6a85db70 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty
| author | fubar |
|---|---|
| date | Fri, 29 Mar 2024 07:27:20 +0000 |
| parents | cefe9dbf1d80 |
| children | 7230a2422507 |
| files | jb210demotracks.jpg jb210demotracks.png jbrowse2.py macros.xml |
| diffstat | 4 files changed, 55 insertions(+), 55 deletions(-) [+] |
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--- a/jbrowse2.py Thu Mar 28 12:17:24 2024 +0000 +++ b/jbrowse2.py Fri Mar 29 07:27:20 2024 +0000 @@ -503,10 +503,6 @@ self.assemblies += assembly self.assmeta[genome_names[0]] = assmeta self.tracksToAdd[genome_names[0]] = [] - if self.config_json.get("assemblies", None): - self.config_json["assemblies"] += assembly - else: - self.config_json["assemblies"] = assembly self.genome_names += genome_names return this_genome["genome_name"] @@ -1124,6 +1120,7 @@ % (pafOpts, pgnames, pgpaths, tId) ) for i, gname in enumerate(pgnames): + lab = trackData["label"] if len(gname.split()) > 1: gname = gname.split()[0] passnames.append(gname) @@ -1135,16 +1132,14 @@ ) 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) + self.tracksToAdd[gname] = [] + self.assemblies.append(asstrack) + if not useuri: + url = "%s.paf" % (lab) + dest = "%s/%s" % (self.outdir, url) + self.symlink_or_copy(os.path.realpath(data), dest) else: - self.config_json["assemblies"] = [ - asstrack, - ] - lab = trackData["label"] - url = "%s.paf" % (lab) - dest = "%s/%s" % (self.outdir, url) - self.symlink_or_copy(os.path.realpath(data), dest) + url = data trackDict = { "type": "SyntenyTrack", "trackId": tId, @@ -1159,6 +1154,10 @@ "assemblyNames": passnames, }, "displays": [ + { + "type": "LGVSyntenyDisplay", + "displayId": "%s-LGVSyntenyDisplay" % lab, + }, {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab}, { "type": "LinearComparativeDisplay", @@ -1168,17 +1167,13 @@ "type": "LinearSyntenyDisplay", "displayId": "%s-LinearSyntenyDisplay" % lab, }, - { - "type": "LGVSyntenyDisplay", - "displayId": "%s-LGVSyntenyDisplay" % lab, - }, ], } style_json = { "displays": [ { - "type": "SyntenyDisplay", - "displayId": "%s-SyntenyDisplay" % lab, + "type": "LGVSyntenyDisplay", + "displayId": "%s-LGVSyntenyDisplay" % lab, } ] } @@ -1341,43 +1336,44 @@ "displays": [style_data], } ) - # The view for the assembly we're adding - view_json = {"type": "LinearGenomeView", "tracks": tracks_data} - refName = self.assmeta[gnome][0].get("genome_firstcontig", None) - drdict = { - "reversed": False, - "assemblyName": gnome, - "start": 1, - "end": 100000, - "refName": refName - } - ddl = default_data.get("defaultLocation", None) - if ddl: - loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) - # allow commas like 100,000 but ignore as integer - if loc_match: - refName = loc_match.group(1) - drdict["refName"] = refName - if loc_match.group(2) > "": - drdict["start"] = int(loc_match.group(2).replace(",", "")) - if loc_match.group(3) > "": - drdict["end"] = int(loc_match.group(3).replace(",", "")) + # paf genomes have no tracks associated so nothing for the view + if len(tracks_data) > 0: + view_json = {"type": "LinearGenomeView", "tracks": tracks_data} + refName = self.assmeta[gnome][0].get("genome_firstcontig", None) + drdict = { + "reversed": False, + "assemblyName": gnome, + "start": 1, + "end": 100000, + "refName": refName + } + ddl = default_data.get("defaultLocation", None) + if ddl: + loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) + # allow commas like 100,000 but ignore as integer + if loc_match: + refName = loc_match.group(1) + drdict["refName"] = refName + if loc_match.group(2) > "": + drdict["start"] = int(loc_match.group(2).replace(",", "")) + if loc_match.group(3) > "": + drdict["end"] = int(loc_match.group(3).replace(",", "")) + else: + logging.info( + "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" + % ddl + ) + if drdict.get("refName", None): + # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome + view_json["displayedRegions"] = [ + drdict, + ] + logging.info("@@@ defaultlocation %s for default session" % drdict) else: logging.info( - "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" - % ddl + "@@@ no contig name found for default session - please add one!" ) - if drdict.get("refName", None): - # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome - view_json["displayedRegions"] = [ - drdict, - ] - logging.info("@@@ defaultlocation %s for default session" % drdict) - else: - logging.info( - "@@@ no contig name found for default session - please add one!" - ) - session_views.append(view_json) + session_views.append(view_json) session_name = default_data.get("session_name", "New session") for key, value in mapped_chars.items(): session_name = session_name.replace(value, key) @@ -1611,9 +1607,13 @@ } jc.add_general_configuration(general_data) trackconf = jc.config_json.get("tracks", []) + logging.warn("genome_names=%s" % jc.genome_names) for gnome in jc.genome_names: trackconf += jc.tracksToAdd[gnome] jc.config_json["tracks"] = trackconf + assconf = jc.config_json.get("assemblies", []) + assconf += jc.assemblies + jc.config_json["assemblies"] = assconf jc.write_config() jc.add_default_session(default_session_data) # jc.text_index() not sure what broke here.
--- a/macros.xml Thu Mar 28 12:17:24 2024 +0000 +++ b/macros.xml Fri Mar 29 07:27:20 2024 +0000 @@ -558,10 +558,10 @@ <when value="history"> <repeat name="refgenomes" title="PAF reference comparison genome used to make the PAF"> <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> - <param label="Short name for track display" name="annoname" type="text" > + <param label="Short name for track display" name="annoname" type="text" help="No spaces allowed here"> <sanitizer invalid_char="_"> <valid initial="string.printable" > - <remove value="'" /> + <remove value=" " /> </valid> </sanitizer> </param>