| Previous changeset 111:0a532764dcfa (2024-07-02) Next changeset 113:878c27dfea9d (2024-07-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792 |
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modified:
jbrowse2.py jbrowse2.xml macros.xml |
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removed:
__pycache__/jbrowse2.cpython-312.pyc |
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| diff -r 0a532764dcfa -r 56f9a6e0fe80 __pycache__/jbrowse2.cpython-312.pyc |
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| Binary file __pycache__/jbrowse2.cpython-312.pyc has changed |
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| diff -r 0a532764dcfa -r 56f9a6e0fe80 jbrowse2.py --- a/jbrowse2.py Tue Jul 02 05:08:17 2024 +0000 +++ b/jbrowse2.py Thu Jul 04 08:40:21 2024 +0000 |
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| @@ -707,7 +707,7 @@ } categ = trackData["category"] fname = tId - dest = "%s/%s" % (self.outdir, fname) + dest = os.path.join(self.outdir, fname) gname = trackData["assemblyNames"] cmd = [ @@ -1074,7 +1074,7 @@ self.trackIdlist.append(tId) def add_bed(self, data, ext, trackData): - bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } } + bedPlugin = {"name": "BedScorePlugin", "umdLoc": {"uri": "bedscoreplugin.js"}} tId = trackData["label"] categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" @@ -1084,16 +1084,16 @@ url = tId + ".gz" dest = os.path.join(self.outdir, url) self._sort_bed(data, dest) - if True or trackData.get("usebedscore",None): + if True or trackData.get("usebedscore", None): bedgzlocation = { - "uri": url, - "columnNames": ["chr","start","end","name","score"], - "scoreColumn": "score", - } + "uri": url, + "columnNames": ["chr", "start", "end", "name", "score"], + "scoreColumn": "score", + } else: bedgzlocation = { - "uri": url, - } + "uri": url, + } trackDict = { "type": "FeatureTrack", "trackId": tId, @@ -1118,7 +1118,7 @@ "renderer": { "type": "SvgFeatureRenderer", "color1": "jexl:customColor(feature)", - }, + }, }, { "type": "LinearPileupDisplay", @@ -1171,7 +1171,7 @@ if gname not in self.genome_names: # ignore if already there - eg for duplicates among pafs. asstrack, first_contig = self.make_assembly(gpath, gname, useuri) - self.genome_names.append(copy.copy(gname)) + self.genome_names.append(gname) self.tracksToAdd[gname] = [] self.assemblies.append(copy.copy(asstrack)) self.ass_first_contigs.append(copy.copy(first_contig)) @@ -1225,7 +1225,7 @@ category = track["category"].replace("__pd__date__pd__", TODAY) tt1 = ",/ :;\\" tt2 = "______" - labttab = str.maketrans(tt1,tt2) + labttab = str.maketrans(tt1, tt2) for trackIndex, ( dataset_path, dataset_ext, @@ -1335,7 +1335,6 @@ else: logging.warning("Do not know how to handle %s", dataset_ext) # Return non-human label for use in other fields - logging.debug("### processanno ext=%s trackstoadd = %s" % (dataset_ext, self.tracksToAdd)) yield outputTrackConfig["label"] def add_default_session(self, default_data): @@ -1344,8 +1343,8 @@ .add_default_view() and other configuration code adapted from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py """ - # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 - bpPerPx = self.bpPerPx # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels. + # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 + bpPerPx = self.bpPerPx # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels. track_types = {} with open(self.config_json_file, "r") as config_file: config_json = json.load(config_file) @@ -1374,7 +1373,7 @@ "style data for %s = %s" % (tId, style_data) ) - if style_data.get('type',None) == None: + if style_data.get('type', None) is None: style_data["type"] = "LinearBasicDisplay" if "displays" in track_conf: disp = track_conf["displays"][0]["type"] @@ -1396,20 +1395,20 @@ ) first = [x for x in self.ass_first_contigs if x[0] == gnome] drdict = { - "reversed": False, - "assemblyName": gnome, - } + "reversed": False, + "assemblyName": gnome, + } if len(first) > 0: [gnome, refName, end] = first[0] drdict["refName"] = refName drdict["start"] = 0 end = int(end) - drdict["end"] = end + drdict["end"] = end else: 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 + # allow commas like 100,000 but ignore as integer if loc_match: refName = loc_match.group(1) drdict["refName"] = refName @@ -1425,7 +1424,7 @@ view_json = { "type": "LinearGenomeView", "offsetPx": 0, - "bpPerPx" : bpPerPx, + "bpPerPx": bpPerPx, "minimized": False, "tracks": tracks_data } @@ -1656,9 +1655,9 @@ for x in trackfiles: isBed = False if x.attrib['ext'] == "bed": - isBed = True + isBed = True track_conf["label"] = "%s_%d" % ( - x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/","_"), + x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/", "_"), trackI, ) trackI += 1 |
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| diff -r 0a532764dcfa -r 56f9a6e0fe80 jbrowse2.xml --- a/jbrowse2.xml Tue Jul 02 05:08:17 2024 +0000 +++ b/jbrowse2.xml Thu Jul 04 08:40:21 2024 +0000 |
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| @@ -8,7 +8,6 @@ <xref type="bio.tools">jbrowse2</xref> </xrefs> <expand macro="requirements"/> - <expand macro="creators"/> <required_files> <include path="autogenJB2.py"/> <include path="blastxml_to_gapped_gff3.py"/> @@ -350,8 +349,7 @@ <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage"> </param> - <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"> - </param> + <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/> </when> </conditional> <repeat name="track_groups" title="Track Group"> @@ -1152,7 +1150,7 @@ Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks. -At present, 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been +Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been used to generate the data: bam @@ -1198,6 +1196,17 @@ Annotation Tracks ----------------- + +BED +~~~ + +Bed feature annotation usually requires clicking on the feature. + +Bed files created by the *Bigwig extremes to bed features* tool have the score in column 5 +set to *1* for regions above the quantile and *-1* for regions below. It is possible to set an advanced option for each bed track, to use the bed score in column 5 +for the feature colour, giving red and blue using a JBrowse2 plugin, so they are easy to distinguish in a combined track. + + MAF ~~~ |
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| diff -r 0a532764dcfa -r 56f9a6e0fe80 macros.xml --- a/macros.xml Tue Jul 02 05:08:17 2024 +0000 +++ b/macros.xml Thu Jul 04 08:40:21 2024 +0000 |
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| @@ -108,7 +108,7 @@ <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing" help="Default is to make an interactive browser appear when the 'eye' icon is activated"/> <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/> <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/> - <param name="bpPerPx" type="integer" value="50" label="Base pairs per display pixel for default view" help="Make the default window show more or less BP of sequence. For some reason not automatable in JB2, sorry"/> + <param name="bpPerPx" type="integer" min="1" value="50" label="Base pairs per display pixel for default view" help="Make the default window show more or less BP of sequence. For some reason not automatable in JB2, sorry"/> <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/> <param name="primary_color" type="color" value="#0D233F" label="Primary color"> <sanitizer> @@ -240,7 +240,8 @@ <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> <option value="LinearArcDisplay">LinearArcDisplay</option> </param> - <param name="usebedscore" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use column 5 as a score for the display if bed format"/> + <param name="usebedscore" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use column 5 as a score for the display if bed format" + help="The *Bigwig extremes to bed features* tool generates bed files with scores 1 or -1. This option renders them red and blue"/> </section> </xml> <xml name="track_styling_feature"> |