Mercurial > repos > fubar > jbrowse2
changeset 59:f807e219cec3 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
| author | fubar |
|---|---|
| date | Fri, 22 Mar 2024 22:04:08 +0000 |
| parents | 0e592dcaeb7f |
| children | 81d535970196 |
| files | jbrowse2.py jbrowse2.xml macros.xml |
| diffstat | 3 files changed, 117 insertions(+), 68 deletions(-) [+] |
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--- a/jbrowse2.py Thu Mar 21 09:06:52 2024 +0000 +++ b/jbrowse2.py Fri Mar 22 22:04:08 2024 +0000 @@ -439,11 +439,13 @@ if trackDict.get("displays", None): # use first if multiple like bed style_data["type"] = trackDict["displays"][0]["type"] style_data["displayId"] = trackDict["displays"][0]["displayId"] - return { + wstyle = { "displays": [ style_data, ] } + logging.warn("style=%s" % (wstyle)) + return wstyle def process_genomes(self): assemblies = [] @@ -496,16 +498,16 @@ "type": "BgzipFastaAdapter", "fastaLocation": { "uri": faname, - "locationType": "UriLocation", + "locationType": "UriLocation" }, "faiLocation": { "uri": faname + ".fai", - "locationType": "UriLocation", + "locationType": "UriLocation" }, "gziLocation": { "uri": faname + ".gzi", - "locationType": "UriLocation", - }, + "locationType": "UriLocation" + } } else: faname = gname + ".fa.gz" @@ -528,7 +530,7 @@ }, "gziLocation": { "uri": faname + ".gzi", - }, + } } trackDict = { @@ -538,7 +540,6 @@ "trackId": gname, "adapter": adapter, }, - "rendering": {"type": "DivSequenceRenderer"}, "displays": [ { "type": "LinearReferenceSequenceDisplay", @@ -548,7 +549,7 @@ "type": "LinearGCContentDisplay", "displayId": "%s-LinearGCContentDisplay" % gname, }, - ], + ] } return trackDict @@ -635,6 +636,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -708,6 +711,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) if self.config_json.get("plugins", None): @@ -781,6 +786,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) os.unlink(gff3) @@ -827,6 +834,8 @@ } ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -880,6 +889,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -928,6 +939,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -980,6 +993,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1041,6 +1056,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1088,6 +1105,8 @@ }, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1095,27 +1114,28 @@ tname = trackData["name"] tId = trackData["label"] categ = trackData["category"] - pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")] - pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] + pgnames = [x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0] + pgpaths = [x.strip() for x in pafOpts["genome"].split(",") if len(x.strip()) > 0] passnames = [self.genome_name] # always first + logging.warn("### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s" % (pafOpts, pgnames, pgpaths, tId)) for i, gname in enumerate(pgnames): if len(gname.split()) > 1: 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"] = [ - asstrack, - ] + 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"] = [ + asstrack, + ] url = "%s.paf" % (trackData["label"]) dest = "%s/%s" % (self.outdir, url) self.symlink_or_copy(os.path.realpath(data), dest) @@ -1131,18 +1151,16 @@ "type": "PAFAdapter", "pafLocation": {"uri": url}, "assemblyNames": passnames, - }, - "displays": [ - { - "type": "LinearSyntenyDisplay", - "displayId": "%s-LinearSyntenyDisplay" % tId, - }, - { - "type": "DotPlotDisplay", - "displayId": "%s-DotPlotDisplay" % tId, - }, - ], + } } + style_json = { + "displays": [ + { "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"] + } + ] + } + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1284,7 +1302,6 @@ if "displays" in track_conf: disp = track_conf["displays"][0]["type"] style_data["type"] = disp - style_data["configuration"] = "%s-%s" % (tId, disp) if track_conf.get("style_labels", None): # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work # TODO move this to per track displays? @@ -1296,7 +1313,6 @@ "displays": [style_data], } ) - # The view for the assembly we're adding view_json = {"type": "LinearGenomeView", "tracks": tracks_data} @@ -1534,9 +1550,6 @@ } else: track_conf["style"] = {} - tst = track_conf["style"].get("type", None) - if tst: - track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst) if track.find("options/style_labels"): track_conf["style_labels"] = { item.tag: parse_style_conf(item) @@ -1565,6 +1578,7 @@ default_session_data["session_name"] = root.find( "metadata/general/session_name" ).text + logging.warn("default_session=%s" % (default_session_data)) jc.zipOut = root.find("metadata/general/zipOut").text == "true" general_data = { "analytics": root.find("metadata/general/analytics").text,
--- a/jbrowse2.xml Thu Mar 21 09:06:52 2024 +0000 +++ b/jbrowse2.xml Fri Mar 22 22:04:08 2024 +0000 @@ -139,16 +139,17 @@ #for $tg in $track_groups: #for $track in $tg.data_tracks: #if $track.data_format.useuri.insource == "uri": - <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> - <files> - <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes"> - <metadata> - <dataset id = "${track.data_format.useuri.annouri}" /> - </metadata> - </trackFile> - </files> - <options/> - </track> + <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}"> + <files> + <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf" + label="${track.data_format.useuri.insource.annoname}" useuri="yes"> + <metadata> + <dataset id = "${track.data_format.useuri.insource.annouri}" /> + </metadata> + </trackFile> + </files> + <options/> + </track> #else if $track.data_format.useuri.insource == "history": #if $track.data_format.useuri.annotation: <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> @@ -203,7 +204,10 @@ #end if #end if #if str($track.data_format.data_format_select) in ["bam", "cram"]: - <type>"LinearAlignmentsDisplay"</type> + <type>LinearAlignmentsDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["paf"]: + <type>LinearBasicDisplay</type> #end if </style> #if str($track.data_format.data_format_select) == "bam": @@ -235,13 +239,13 @@ #else if str($track.data_format.data_format_select) == "paf": <paf> <genome> - #for gnome in $track.data_format.synteny_genome: - $gnome, + #for refgenome in $track.data_format.pafuseuri.refgenomes: + $refgenome.annotation, #end for </genome> <genome_label> - #for gnome in $track.data_format.synteny_genome: - $gnome.name, + #for refgenome in $track.data_format.pafuseuri.refgenomes: + $refgenome.annoname, #end for </genome_label> </paf> @@ -327,17 +331,17 @@ <repeat name="data_tracks" title="Annotation Track"> <conditional name="data_format" label="Track Data Selection Options"> <param type="select" label="Track Type" name="data_format_select"> - <option value="bam">BAM Pileup track</option> + <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option> <option value="bed">BED track</option> <option value="bigwig">BigWig track</option> - <option value="blastxml">Blast XML track - converted to GFF</option> + <option value="blastxml">Blast XML track (as GFF3)</option> + <option value="cram">CRAM track. Currently not advantageous over BAM in Galaxy. Convert to BED like BAM.</option> + <option value="gff">GFF/GFF3 track</option> <option value="cool">HiC as cool/mcool/scool format files</option> - <option value="cram">CRAM</option> - <option value="gff">GFF/GFF3 feature track</option> <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> <option value="paf">PAF - approximate mapping positions between two set of sequences</option> - <option value="vcf">VCF SNP</option> + <option value="vcf">VCF SNP track</option> </param> <when value="blastxml"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> @@ -411,12 +415,10 @@ <expand macro="track_visibility" /> </when> <when value="paf"> - <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map" - format="fasta" - name="synteny_genome" - type="data" - multiple="True"/> - <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/> + <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" + help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/> + <expand macro="pafref_conditional" label="Comparison genome sequence(s)" + format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/> <expand macro="track_visibility" /> </when>
--- a/macros.xml Thu Mar 21 09:06:52 2024 +0000 +++ b/macros.xml Fri Mar 22 22:04:08 2024 +0000 @@ -522,7 +522,7 @@ <param name="insource" type="select" label="Define track data as a history file or an internet URI" help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> <option value="history" selected="true">Track data from a history file</option> - <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option> + <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> </param> <when value="history"> <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> @@ -539,6 +539,39 @@ </when> </conditional> </xml> + <xml name="pafref_conditional" token_label="Track Data" token_format="data"> + <conditional name="pafuseuri"> + <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" + help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> + <option value="history" selected="true">PAF genome reference data from a history file</option> + <option value="uri">PAF genome reference data from tabix data URI - index files must be available at corresponding URI</option> + </param> + <when value="history"> + <repeat name="refgenomes" title="Add one or more comparison genomes 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" > + <sanitizer invalid_char="_"> + <valid initial="string.printable" > + <remove value="'" /> + </valid> + </sanitizer> + </param> + </repeat> + </when> + <when value="uri"> + <repeat name="refgenomes" title="Provide URI for a comparison genomesused to make the PAF"> + <param label="@LABEL@" name="annotation" type="text" /> + <param label="Short name for track display" name="annoname" type="text" > + <sanitizer invalid_char="_"> + <valid initial="string.printable" > + <remove value="'" /> + </valid> + </sanitizer> + </param> + </repeat> + </when> + </conditional> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-016-0924-1</citation>