Mercurial > repos > fubar > jbrowse2
changeset 57:94264fe60478 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
| author | fubar |
|---|---|
| date | Thu, 21 Mar 2024 08:01:42 +0000 |
| parents | c0097a584a8a |
| children | 0e592dcaeb7f |
| files | autogenJB2.py convertMAF.sh jb2_urlconf.py jbrowse2.py jbrowse2.xml jbrowse2broken.py jbrowse2broken.xml macrosbroken.xml test-data/gff3/merlin.gff3 |
| diffstat | 9 files changed, 3382 insertions(+), 181 deletions(-) [+] |
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--- a/autogenJB2.py Tue Mar 19 02:33:40 2024 +0000 +++ b/autogenJB2.py Thu Mar 21 08:01:42 2024 +0000 @@ -61,10 +61,10 @@ genome_names = [x[2] for x in listgenomes] guseuri = [] for x in genome_paths: - if x.startswith('http://') or x.startswith('https://'): - guseuri.append('yes') + if x.startswith("http://") or x.startswith("https://"): + guseuri.append("yes") else: - guseuri.append('no') + guseuri.append("no") jc = jbC( outdir=args.outdir, jbrowse2path=args.jbrowse2path, @@ -73,9 +73,10 @@ "path": x, "label": genome_names[i], "useuri": guseuri[i], - "meta": {"name": genome_names[i], - "dataset_dname": genome_names[i] - } + "meta": { + "name": genome_names[i], + "dataset_dname": genome_names[i], + }, } for i, x in enumerate(genome_paths) ], @@ -99,7 +100,7 @@ tpath, trext, trackname = track[:3] track_conf["dataset_id"] = trackname useuri = "no" - if tpath.startswith('http://') or tpath.startswith('https://'): + if tpath.startswith("http://") or tpath.startswith("https://"): useuri = "yes" if trext == "paf": refname = trackname + "_paf.fasta" @@ -111,28 +112,55 @@ ) sys.exit(3) else: - track_conf.update({ - "conf": { - "options": { - "paf": {"genome": refdat, "genome_label": trackname} + track_conf.update( + { + "conf": { + "options": { + "paf": { + "genome": refdat, + "genome_label": trackname, + } + } } } - }) + ) elif trext == "bam": - ipath = track[3] + ipath = track[3] if not os.path.exists(ipath): - ipath = os.path.realpath(os.path.join(jc.outdir, trackname + '.bai')) - cmd = ["samtools", "index", "-b", "-o", ipath, os.path.realpath(track[0])] - sys.stdout.write('#### calling %s' % ' '.join(cmd)) + ipath = os.path.realpath( + os.path.join(jc.outdir, trackname + ".bai") + ) + cmd = [ + "samtools", + "index", + "-b", + "-o", + ipath, + os.path.realpath(track[0]), + ] + sys.stdout.write("#### calling %s" % " ".join(cmd)) jc.subprocess_check_call(cmd) - track_conf.update({"conf": {"options": {"bam": {"bam_index": ipath}}}}) + track_conf.update( + {"conf": {"options": {"bam": {"bam_index": ipath}}}} + ) elif trext == "cram": - ipath = track[3] + ipath = track[3] if not os.path.exists(ipath): - ipath = os.path.realpath(os.path.join('./', trackname + '.crai')) - cmd = ["samtools", "index", "-c", "-o", ipath, os.path.realpath(track[0])] + ipath = os.path.realpath( + os.path.join("./", trackname + ".crai") + ) + cmd = [ + "samtools", + "index", + "-c", + "-o", + ipath, + os.path.realpath(track[0]), + ] jc.subprocess_check_call(cmd) - track_conf.update({"conf": {"options": {"cram": {"cram_index": ipath}}}}) + track_conf.update( + {"conf": {"options": {"cram": {"cram_index": ipath}}}} + ) track_conf["path"] = tpath track_conf["format"] = trext track_conf["name"] = trackname
--- a/convertMAF.sh Tue Mar 19 02:33:40 2024 +0000 +++ b/convertMAF.sh Thu Mar 21 08:01:42 2024 +0000 @@ -3,5 +3,5 @@ # MAF file must contain the species name and chromosome name # e.g. hg38.chr1 in the sequence identifiers. perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed -bgzip $4.sorted.bed +bgzip -c $4.sorted.bed > $4.sorted.bed.gz tabix -p bed $4.sorted.bed.gz
--- a/jb2_urlconf.py Tue Mar 19 02:33:40 2024 +0000 +++ b/jb2_urlconf.py Thu Mar 21 08:01:42 2024 +0000 @@ -1,18 +1,13 @@ - -inconf = open('config.json', 'r').readlines() -with open('config.json.local', 'w') as bak: - bak.write(''.join(inconf)) +inconf = open("config.json", "r").readlines() +with open("config.json.local", "w") as bak: + bak.write("".join(inconf)) urlbase = "https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/hum/" utag = '"uri":' for i, row in enumerate(inconf): ispath = False if row.strip().startswith(utag): - ispath = True - parth = row.split(utag)[1].strip().replace('"','').replace("'",'') - inconf[i] = '%s "%s%s"' % (utag, urlbase, parth) -with open('config.json', 'w') as outconf: - outconf.write(''.join(inconf)) - - - - + ispath = True + parth = row.split(utag)[1].strip().replace('"', "").replace("'", "") + inconf[i] = '%s "%s%s"' % (utag, urlbase, parth) +with open("config.json", "w") as outconf: + outconf.write("".join(inconf))
--- a/jbrowse2.py Tue Mar 19 02:33:40 2024 +0000 +++ b/jbrowse2.py Thu Mar 21 08:01:42 2024 +0000 @@ -1,4 +1,4 @@ -#!/usr/bin/env python + #!/usr/bin/env python # change to accumulating all configuration for config.json based on the default from the clone import argparse import binascii @@ -10,7 +10,6 @@ import shutil import struct import subprocess -import sys import tempfile import urllib.request import xml.etree.ElementTree as ET @@ -480,9 +479,11 @@ else: self.genome_firstcontig = fl else: - fl = urllib.request.urlopen(fapath+".fai").readline() - if fl: # is first row of the text fai so the first contig name - self.genome_firstcontig = fl.decode('utf8').strip().split()[0] + fl = urllib.request.urlopen(fapath + ".fai").readline() + if fl: # is first row of the text fai so the first contig name + self.genome_firstcontig = ( + fl.decode("utf8").strip().split()[0] + ) if self.config_json.get("assemblies", None): self.config_json["assemblies"] += assemblies else: @@ -538,6 +539,16 @@ "adapter": adapter, }, "rendering": {"type": "DivSequenceRenderer"}, + "displays": [ + { + "type": "LinearReferenceSequenceDisplay", + "displayId": "%s-LinearReferenceSequenceDisplay" % gname, + }, + { + "type": "LinearGCContentDisplay", + "displayId": "%s-LinearGCContentDisplay" % gname, + }, + ], } return trackDict @@ -604,13 +615,15 @@ uri = data else: uri = trackData["hic_url"] - categ = trackData['category'] + categ = trackData["category"] trackDict = { "type": "HicTrack", "trackId": tId, "name": uri, "assemblyNames": [self.genome_name], - "category": [categ,], + "category": [ + categ, + ], "adapter": { "type": "HicAdapter", "hicLocation": uri, @@ -622,8 +635,6 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -643,7 +654,7 @@ } ] } - categ = trackData['category'] + categ = trackData["category"] fname = "%s.bed" % tId dest = "%s/%s" % (self.outdir, fname) gname = self.genome_name @@ -665,11 +676,14 @@ soutp = outp.split("\n") samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")] samples = [x.split(".")[0] for x in samp] + logging.warn("### maf convert cmd = %s,\nsamples=%s" % (' '.join(cmd), samples)) trackDict = { "type": "MafTrack", "trackId": tId, "name": trackData["name"], - "category": [categ,], + "category": [ + categ, + ], "adapter": { "type": "MafTabixAdapter", "samples": samples, @@ -694,8 +708,6 @@ }, ], } - 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): @@ -717,11 +729,11 @@ ] subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) gff3_unrebased.close() + logging.warn("### blastxml to gff3 cmd = %s" % ' '.join(cmd)) return gff3_unrebased.name def add_blastxml(self, data, trackData, blastOpts, **kwargs): gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"]) - if "parent" in blastOpts and blastOpts["parent"] != "None": gff3_rebased = tempfile.NamedTemporaryFile(delete=False) cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")] @@ -729,23 +741,24 @@ cmd.append("--protein2dna") cmd.extend([os.path.realpath(blastOpts["parent"]), gff3]) subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) + logging.warn("### gff3rebase cmd = %s" % ' '.join(cmd)) gff3_rebased.close() - # Replace original gff3 file shutil.copy(gff3_rebased.name, gff3) os.unlink(gff3_rebased.name) - url = "%s.gff3" % trackData["label"] + url = "%s.gff3.gz" % trackData["label"] dest = "%s/%s" % (self.outdir, url) self._sort_gff(gff3, dest) - url = url + ".gz" tId = trackData["label"] - categ = trackData['category'] + categ = trackData["category"] trackDict = { "type": "FeatureTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [self.genome_name], - "category": [categ,], + "category": [ + categ, + ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { @@ -768,8 +781,6 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) os.unlink(gff3) @@ -794,12 +805,14 @@ self.subprocess_check_call(cmd) bwloc = {"uri": url} tId = trackData["label"] - categ = trackData['category'] + categ = trackData["category"] trackDict = { "type": "QuantitativeTrack", "trackId": tId, "name": trackData["name"], - "category": [categ,], + "category": [ + categ, + ], "assemblyNames": [ self.genome_name, ], @@ -814,8 +827,6 @@ } ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -823,21 +834,19 @@ tId = trackData["label"] useuri = trackData["useuri"].lower() == "yes" bindex = bam_index - categ = trackData['category'] + categ = trackData["category"] if useuri: url = data else: fname = "%s.bam" % trackData["label"] dest = "%s/%s" % (self.outdir, fname) url = fname - bindex = fname + '.bai' + bindex = fname + ".bai" self.subprocess_check_call(["cp", data, dest]) if bam_index is not None and os.path.exists(bam_index): if not os.path.exists(bindex): # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest - self.subprocess_check_call( - ["cp", bam_index, bindex] - ) + self.subprocess_check_call(["cp", bam_index, bindex]) else: # Can happen in exotic condition # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam @@ -851,7 +860,9 @@ "type": "AlignmentsTrack", "trackId": tId, "name": trackData["name"], - "category": [categ,], + "category": [ + categ, + ], "assemblyNames": [self.genome_name], "adapter": { "type": "BamAdapter", @@ -869,14 +880,12 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) def add_cram(self, data, trackData, cram_index=None, **kwargs): tId = trackData["label"] - categ = trackData['category'] + categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = data @@ -886,27 +895,29 @@ url = fname self.subprocess_check_call(["cp", data, dest]) if cram_index is not None and os.path.exists(cram_index): - if not os.path.exists(dest+'.crai'): + if not os.path.exists(dest + ".crai"): # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest self.subprocess_check_call( ["cp", os.path.realpath(cram_index), dest + ".crai"] ) else: - cpath = os.path.realpath(dest) + '.crai' + cpath = os.path.realpath(dest) + ".crai" cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)] - logging.debug('executing cmd %s' % ' '.join(cmd)) + logging.debug("executing cmd %s" % " ".join(cmd)) self.subprocess_check_call(cmd) trackDict = { "type": "AlignmentsTrack", "trackId": tId, "name": trackData["name"], - "category": [categ,], + "category": [ + categ, + ], "assemblyNames": [self.genome_name], "adapter": { "type": "CramAdapter", "cramLocation": {"uri": url}, "craiLocation": { - "uri": url + '.crai', + "uri": url + ".crai", }, "sequenceAdapter": self.genome_sequence_adapter, }, @@ -917,8 +928,6 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -928,7 +937,7 @@ # self.giURL, # trackData["metadata"]["dataset_id"], # ) - categ = trackData['category'] + categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = data @@ -944,12 +953,12 @@ "trackId": tId, "name": trackData["name"], "assemblyNames": [self.genome_name], - "category": [categ,], + "category": [ + categ, + ], "adapter": { "type": "VcfTabixAdapter", - "vcfGzLocation": { - "uri": url - }, + "vcfGzLocation": {"uri": url}, "index": { "location": { "uri": url + ".tbi", @@ -971,8 +980,6 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1003,13 +1010,15 @@ dest = "%s/%s" % (self.outdir, url) self._sort_gff(data, dest) tId = trackData["label"] - categ = trackData['category'] + categ = trackData["category"] trackDict = { "type": "FeatureTrack", "trackId": tId, "name": trackData["name"], "assemblyNames": [self.genome_name], - "category": [categ,], + "category": [ + categ, + ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { @@ -1032,14 +1041,12 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) def add_bed(self, data, ext, trackData): tId = trackData["label"] - categ = trackData['category'] + categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" if useuri: url = data @@ -1053,7 +1060,9 @@ "name": trackData["name"], "assemblyNames": [self.genome_name], "adapter": { - "category": [categ,], + "category": [ + categ, + ], "type": "BedTabixAdapter", "bedGzLocation": { "uri": url, @@ -1079,15 +1088,13 @@ }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) def add_paf(self, data, trackData, pafOpts, **kwargs): tname = trackData["name"] tId = trackData["label"] - categ = trackData['category'] + categ = trackData["category"] pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")] pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] passnames = [self.genome_name] # always first @@ -1098,7 +1105,9 @@ # 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://') + 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): @@ -1114,7 +1123,9 @@ "type": "SyntenyTrack", "trackId": tId, "assemblyNames": passnames, - "category": [categ,], + "category": [ + categ, + ], "name": tname, "adapter": { "type": "PAFAdapter", @@ -1122,18 +1133,16 @@ "assemblyNames": passnames, }, "displays": [ - { - "type": "LinearSyntenyDisplay", - "displayId": "%s-LinearSyntenyDisplay" % tId, - }, - { - "type": "DotPlotDisplay", - "displayId": "%s-DotPlotDisplay" % tId, - }, + { + "type": "LinearSyntenyDisplay", + "displayId": "%s-LinearSyntenyDisplay" % tId, + }, + { + "type": "DotPlotDisplay", + "displayId": "%s-DotPlotDisplay" % tId, + }, ], } - style_json = self._prepare_track_style(trackDict) - trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1249,7 +1258,7 @@ # Return non-human label for use in other fields yield outputTrackConfig["label"] - def add_default_session(self, data): + def add_default_session(self, default_data): """ Add some default session settings: set some assemblies/tracks on/off """ @@ -1267,21 +1276,26 @@ for track_conf in self.tracksToAdd: track_types[track_conf["trackId"]] = track_conf["type"] tId = track_conf["trackId"] - if tId in data["visibility"]["default_on"]: + #if tId in data["visibility"]["default_on"]: + style_data = default_data["style"].get(tId, None) + if not style_data: + logging.warn("### No style data in default data for %s" % tId) style_data = {"type": "LinearBasicDisplay"} - if "displays" in track_conf: - style_data["type"] = track_conf["displays"][0]["type"] - 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? - style_data["labels"] = track_conf["style_labels"] - tracks_data.append( - { - "type": track_types[tId], - "configuration": tId, - "displays": [style_data], - } - ) + 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? + style_data["labels"] = track_conf["style_labels"] + tracks_data.append( + { + "type": track_types[tId], + "configuration": tId, + "displays": [style_data], + } + ) # The view for the assembly we're adding view_json = {"type": "LinearGenomeView", "tracks": tracks_data} @@ -1290,13 +1304,13 @@ drdict = { "reversed": False, "assemblyName": self.genome_name, - "start": 2000, - "end": 200000, + "start": 1, + "end": 100000, "refName": "x", } - if data.get("defaultLocation", ""): - ddl = data["defaultLocation"] + if default_data.get("defaultLocation", ""): + ddl = default_data["defaultLocation"] loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) # allow commas like 100,000 but ignore as integer if loc_match: @@ -1324,7 +1338,7 @@ logging.info( "@@@ no contig name found for default session - please add one!" ) - session_name = data.get("session_name", "New session") + session_name = default_data.get("session_name", "New session") for key, value in mapped_chars.items(): session_name = session_name.replace(value, key) # Merge with possibly existing defaultSession (if upgrading a jbrowse instance) @@ -1382,7 +1396,9 @@ """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now""" dest = self.outdir if realclone: - self.subprocess_check_call(['jbrowse', 'create', dest,"-f", '--tag', f"{JB2VER}"]) + self.subprocess_check_call( + ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"] + ) else: shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True) for fn in [ @@ -1400,14 +1416,8 @@ def parse_style_conf(item): - if "type" in item.attrib and item.attrib["type"] in [ - "boolean", - "integer", - ]: - if item.attrib["type"] == "boolean": - return item.text in ("yes", "true", "True") - elif item.attrib["type"] == "integer": - return int(item.text) + if item.text.lower() in ['false','true','yes','no']: + return item.text.lower in ("yes", "true") else: return item.text @@ -1473,6 +1483,7 @@ trackfiles = track.findall("files/trackFile") if trackfiles: for x in track.findall("files/trackFile"): + track_conf["label"] = x.attrib["label"] track_conf["useuri"] = x.attrib["useuri"] if is_multi_bigwig: multi_bigwig_paths.append( @@ -1521,6 +1532,11 @@ track_conf["style"] = { item.tag: parse_style_conf(item) for item in track.find("options/style") } + 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) @@ -1530,12 +1546,6 @@ track_conf["conf"] = etree_to_dict(track.find("options")) track_conf["category"] = track.attrib["cat"] track_conf["format"] = track.attrib["format"] - try: - # Only pertains to gff3 + blastxml. TODO? - track_conf["style"] = {t.tag: t.text for t in track.find("options/style")} - except TypeError: - track_conf["style"] = {} - pass keys = jc.process_annotations(track_conf) if keys: @@ -1544,9 +1554,7 @@ track.attrib.get("visibility", "default_off") ].append(key) if track_conf.get("style", None): - default_session_data["style"][key] = track_conf[ - "style" - ] # TODO do we need this anymore? + default_session_data["style"][key] = track_conf["style"] if track_conf.get("style_lables", None): default_session_data["style_labels"][key] = track_conf.get( "style_labels", None
--- a/jbrowse2.xml Tue Mar 19 02:33:40 2024 +0000 +++ b/jbrowse2.xml Thu Mar 21 08:01:42 2024 +0000 @@ -194,7 +194,18 @@ </files> <options> - + <style> + #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "paf", "maf", "blastxml"]: + <type>${track.data_format.jbstyle.track_style.display}</type> + #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: + <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> + <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> + #end if + #end if + #if str($track.data_format.data_format_select) in ["bam", "cram"]: + <type>"LinearAlignmentsDisplay"</type> + #end if + </style> #if str($track.data_format.data_format_select) == "bam": <bam> #for $dataset in $track.data_format.useuri.annotation: @@ -349,6 +360,7 @@ name="is_protein" truevalue="true" falsevalue="false" /> + <expand macro="track_styling_feature" /> <expand macro="track_visibility" /> </when> <when value="vcf"> @@ -373,6 +385,7 @@ </when> <when value="false" /> </conditional> + <expand macro="track_styling_feature" /> <expand macro="track_visibility" /> </when> <when value="bam"> @@ -381,6 +394,7 @@ </when> <when value="bed"> <expand macro="input_conditional" label="BED Track Data" format="bed" /> + <expand macro="track_styling_feature" /> <expand macro="track_visibility" /> </when> <when value="cram"> @@ -389,6 +403,7 @@ </when> <when value="maf"> <expand macro="input_conditional" label="MAF Track Data" format="maf" /> + <expand macro="track_styling_feature" /> <expand macro="track_visibility" /> </when> <when value="bigwig">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse2broken.py Thu Mar 21 08:01:42 2024 +0000 @@ -0,0 +1,1656 @@ +#!/usr/bin/env python +# change to accumulating all configuration for config.json based on the default from the clone +import argparse +import binascii +import datetime +import json +import logging +import os +import re +import shutil +import struct +import subprocess +import tempfile +import urllib.request +import xml.etree.ElementTree as ET +from collections import defaultdict + +logging.basicConfig(level=logging.INFO) +log = logging.getLogger("jbrowse") + +JB2VER = "v2.10.3" +# version pinned for cloning + +TODAY = datetime.datetime.now().strftime("%Y-%m-%d") +GALAXY_INFRASTRUCTURE_URL = None + +# version pinned for cloning + +mapped_chars = { + ">": "__gt__", + "<": "__lt__", + "'": "__sq__", + '"': "__dq__", + "[": "__ob__", + "]": "__cb__", + "{": "__oc__", + "}": "__cc__", + "@": "__at__", + "#": "__pd__", + "": "__cn__", +} + + +class ColorScaling(object): + + COLOR_FUNCTION_TEMPLATE = """ + function(feature, variableName, glyphObject, track) {{ + var score = {score}; + {opacity} + return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; + }} + """ + + COLOR_FUNCTION_TEMPLATE_QUAL = r""" + function(feature, variableName, glyphObject, track) {{ + var search_up = function self(sf, attr){{ + if(sf.get(attr) !== undefined){{ + return sf.get(attr); + }} + if(sf.parent() === undefined) {{ + return; + }}else{{ + return self(sf.parent(), attr); + }} + }}; + + var search_down = function self(sf, attr){{ + if(sf.get(attr) !== undefined){{ + return sf.get(attr); + }} + if(sf.children() === undefined) {{ + return; + }}else{{ + var kids = sf.children(); + for(var child_idx in kids){{ + var x = self(kids[child_idx], attr); + if(x !== undefined){{ + return x; + }} + }} + return; + }} + }}; + + var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); + var score = (search_up(feature, 'score') || search_down(feature, 'score')); + {opacity} + if(score === undefined){{ opacity = 1; }} + var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); + var red = parseInt(result[1], 16); + var green = parseInt(result[2], 16); + var blue = parseInt(result[3], 16); + if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} + return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; + }} + """ + + OPACITY_MATH = { + "linear": """ + var opacity = (score - ({min})) / (({max}) - ({min})); + """, + "logarithmic": """ + var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min})); + """, + "blast": """ + var opacity = 0; + if(score == 0.0) {{ + opacity = 1; + }} else {{ + opacity = (20 - Math.log10(score)) / 180; + }} + """, + } + + BREWER_COLOUR_IDX = 0 + BREWER_COLOUR_SCHEMES = [ + (166, 206, 227), + (31, 120, 180), + (178, 223, 138), + (51, 160, 44), + (251, 154, 153), + (227, 26, 28), + (253, 191, 111), + (255, 127, 0), + (202, 178, 214), + (106, 61, 154), + (255, 255, 153), + (177, 89, 40), + (228, 26, 28), + (55, 126, 184), + (77, 175, 74), + (152, 78, 163), + (255, 127, 0), + ] + + BREWER_DIVERGING_PALLETES = { + "BrBg": ("#543005", "#003c30"), + "PiYg": ("#8e0152", "#276419"), + "PRGn": ("#40004b", "#00441b"), + "PuOr": ("#7f3b08", "#2d004b"), + "RdBu": ("#67001f", "#053061"), + "RdGy": ("#67001f", "#1a1a1a"), + "RdYlBu": ("#a50026", "#313695"), + "RdYlGn": ("#a50026", "#006837"), + "Spectral": ("#9e0142", "#5e4fa2"), + } + + def __init__(self): + self.brewer_colour_idx = 0 + + def rgb_from_hex(self, hexstr): + # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back + return struct.unpack("BBB", binascii.unhexlify(hexstr)) + + def min_max_gff(self, gff_file): + min_val = None + max_val = None + with open(gff_file, "r") as handle: + for line in handle: + try: + value = float(line.split("\t")[5]) + min_val = min(value, (min_val or value)) + max_val = max(value, (max_val or value)) + + if value < min_val: + min_val = value + + if value > max_val: + max_val = value + except Exception: + pass + return min_val, max_val + + def hex_from_rgb(self, r, g, b): + return "#%02x%02x%02x" % (r, g, b) + + def _get_colours(self): + r, g, b = self.BREWER_COLOUR_SCHEMES[ + self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES) + ] + self.brewer_colour_idx += 1 + return r, g, b + + def parse_menus(self, track): + trackConfig = {"menuTemplate": [{}, {}, {}, {}]} + + if "menu" in track["menus"]: + menu_list = [track["menus"]["menu"]] + if isinstance(track["menus"]["menu"], list): + menu_list = track["menus"]["menu"] + + for m in menu_list: + tpl = { + "action": m["action"], + "label": m.get("label", "{name}"), + "iconClass": m.get("iconClass", "dijitIconBookmark"), + } + if "url" in m: + tpl["url"] = m["url"] + if "content" in m: + tpl["content"] = m["content"] + if "title" in m: + tpl["title"] = m["title"] + + trackConfig["menuTemplate"].append(tpl) + + return trackConfig + + def parse_colours(self, track, trackFormat, gff3=None): + # Wiggle tracks have a bicolor pallete + trackConfig = {"style": {}} + if trackFormat == "wiggle": + + trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"] + trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"] + + if trackConfig["style"]["pos_color"] == "__auto__": + trackConfig["style"]["neg_color"] = self.hex_from_rgb( + *self._get_colours() + ) + trackConfig["style"]["pos_color"] = self.hex_from_rgb( + *self._get_colours() + ) + + # Wiggle tracks can change colour at a specified place + bc_pivot = track["wiggle"]["bicolor_pivot"] + if bc_pivot not in ("mean", "zero"): + # The values are either one of those two strings + # or a number + bc_pivot = float(bc_pivot) + trackConfig["bicolor_pivot"] = bc_pivot + elif "scaling" in track: + if track["scaling"]["method"] == "ignore": + if track["scaling"]["scheme"]["color"] != "__auto__": + trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"] + else: + trackConfig["style"]["color"] = self.hex_from_rgb( + *self._get_colours() + ) + else: + # Scored method + algo = track["scaling"]["algo"] + # linear, logarithmic, blast + scales = track["scaling"]["scales"] + # type __auto__, manual (min, max) + scheme = track["scaling"]["scheme"] + # scheme -> (type (opacity), color) + # ================================== + # GENE CALLS OR BLAST + # ================================== + if trackFormat == "blast": + red, green, blue = self._get_colours() + color_function = self.COLOR_FUNCTION_TEMPLATE.format( + **{ + "score": "feature._parent.get('score')", + "opacity": self.OPACITY_MATH["blast"], + "red": red, + "green": green, + "blue": blue, + } + ) + trackConfig["style"]["color"] = color_function.replace("\n", "") + elif trackFormat == "gene_calls": + # Default values, based on GFF3 spec + min_val = 0 + max_val = 1000 + # Get min/max and build a scoring function since JBrowse doesn't + if scales["type"] == "automatic" or scales["type"] == "__auto__": + min_val, max_val = self.min_max_gff(gff3) + else: + min_val = scales.get("min", 0) + max_val = scales.get("max", 1000) + + if scheme["color"] == "__auto__": + user_color = "undefined" + auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) + elif scheme["color"].startswith("#"): + user_color = "'%s'" % self.hex_from_rgb( + *self.rgb_from_hex(scheme["color"][1:]) + ) + auto_color = "undefined" + else: + user_color = "undefined" + auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) + + color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format( + **{ + "opacity": self.OPACITY_MATH[algo].format( + **{"max": max_val, "min": min_val} + ), + "user_spec_color": user_color, + "auto_gen_color": auto_color, + } + ) + + trackConfig["style"]["color"] = color_function.replace("\n", "") + return trackConfig + + +def etree_to_dict(t): + if t is None: + return {} + + d = {t.tag: {} if t.attrib else None} + children = list(t) + if children: + dd = defaultdict(list) + for dc in map(etree_to_dict, children): + for k, v in dc.items(): + dd[k].append(v) + d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} + if t.attrib: + d[t.tag].update(("@" + k, v) for k, v in t.attrib.items()) + if t.text: + text = t.text.strip() + if children or t.attrib: + if text: + d[t.tag]["#text"] = text + else: + d[t.tag] = text + return d + + +INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) + + +def metadata_from_node(node): + metadata = {} + try: + if len(node.findall("dataset")) != 1: + # exit early + return metadata + except Exception: + return {} + + for (key, value) in node.findall("dataset")[0].attrib.items(): + metadata["dataset_%s" % key] = value + + if node.findall("history"): + for (key, value) in node.findall("history")[0].attrib.items(): + metadata["history_%s" % key] = value + + if node.findall("metadata"): + for (key, value) in node.findall("metadata")[0].attrib.items(): + metadata["metadata_%s" % key] = value + # Additional Mappings applied: + metadata[ + "dataset_edam_format" + ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format( + metadata["dataset_edam_format"], metadata["dataset_file_ext"] + ) + metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format( + metadata["history_user_email"] + ) + metadata["hist_name"] = metadata["history_display_name"] + metadata[ + "history_display_name" + ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( + galaxy=GALAXY_INFRASTRUCTURE_URL, + encoded_hist_id=metadata["history_id"], + hist_name=metadata["history_display_name"], + ) + if node.findall("tool"): + for (key, value) in node.findall("tool")[0].attrib.items(): + metadata["tool_%s" % key] = value + metadata[ + "tool_tool" + ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}{tool_version}</a>'.format( + galaxy=GALAXY_INFRASTRUCTURE_URL, + encoded_id=metadata.get("dataset_id", ""), + tool_id=metadata.get("tool_tool_id", ""), + tool_version=metadata.get("tool_tool_version", ""), + ) + return metadata + + +class JbrowseConnector(object): + def __init__(self, outdir, jbrowse2path, genomes): + self.giURL = GALAXY_INFRASTRUCTURE_URL + self.outdir = outdir + self.jbrowse2path = jbrowse2path + os.makedirs(self.outdir, exist_ok=True) + self.genome_paths = genomes + self.genome_name = None + self.genome_names = [] + self.trackIdlist = [] + self.tracksToAdd = [] + self.config_json = {} + self.config_json_file = os.path.join(outdir, "config.json") + self.clone_jbrowse() + + def subprocess_check_call(self, command, output=None): + if output: + log.debug("cd %s && %s > %s", self.outdir, " ".join(command), output) + subprocess.check_call(command, cwd=self.outdir, stdout=output) + else: + log.debug("cd %s && %s", self.outdir, " ".join(command)) + subprocess.check_call(command, cwd=self.outdir) + + def subprocess_popen(self, command): + log.debug(command) + p = subprocess.Popen( + command, + cwd=self.outdir, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + output, err = p.communicate() + retcode = p.returncode + if retcode != 0: + log.error(command) + log.error(output) + log.error(err) + raise RuntimeError("Command failed with exit code %s" % (retcode)) + + def _prepare_track_style(self, trackDict): + style_data = { + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"], + } + + 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 { + "displays": [ + style_data, + ] + } + + def subprocess_check_output(self, command): + log.debug(" ".join(command)) + return subprocess.check_output(command, cwd=self.outdir) + + def symlink_or_copy(self, src, dest): + if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool( + os.environ["GALAXY_JBROWSE_SYMLINKS"] + ): + cmd = ["ln", "-s", src, dest] + else: + cmd = ["cp", src, dest] + + return self.subprocess_check_call(cmd) + + def process_genomes(self): + assemblies = [] + useuri = False + for i, genome_node in enumerate(self.genome_paths): + if genome_node["useuri"].strip().lower() == "yes": + useuri = True + genome_name = genome_node["meta"]["dataset_dname"].strip() + if len(genome_name.split()) > 1: + genome_name = genome_name.split()[0] + # spaces and cruft break scripts when substituted + if genome_name not in self.genome_names: + # ignore dupes - can have multiple pafs with same references? + fapath = genome_node["path"] + if not useuri: + fapath = os.path.realpath(fapath) + assem = self.make_assembly(fapath, genome_name, useuri) + assemblies.append(assem) + self.genome_names.append(genome_name) + if self.genome_name is None: + self.genome_name = ( + genome_name # first one for all tracks - other than paf + ) + self.genome_sequence_adapter = assem["sequence"]["adapter"] + self.genome_firstcontig = None + if not useuri: + fl = open(fapath, "r").readline() + fls = fl.strip().split(">") + if len(fls) > 1: + fl = fls[1] + if len(fl.split()) > 1: + self.genome_firstcontig = fl.split()[0].strip() + else: + self.genome_firstcontig = fl + else: + fl = urllib.request.urlopen(fapath + ".fai").readline() + if fl: # is first row of the text fai so the first contig name + self.genome_firstcontig = ( + fl.decode("utf8").strip().split()[0] + ) + if self.config_json.get("assemblies", None): + self.config_json["assemblies"] += assemblies + else: + self.config_json["assemblies"] = assemblies + + def make_assembly(self, fapath, gname, useuri): + if useuri: + faname = fapath + adapter = { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": faname, + "locationType": "UriLocation", + }, + "faiLocation": { + "uri": faname + ".fai", + "locationType": "UriLocation", + }, + "gziLocation": { + "uri": faname + ".gzi", + "locationType": "UriLocation", + }, + } + else: + faname = gname + ".fa.gz" + fadest = os.path.realpath(os.path.join(self.outdir, faname)) + cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % ( + fapath, + fadest, + fadest, + fadest, + ) + self.subprocess_popen(cmd) + + adapter = { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": faname, + }, + "faiLocation": { + "uri": faname + ".fai", + }, + "gziLocation": { + "uri": faname + ".gzi", + }, + } + + trackDict = { + "name": gname, + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": gname, + "adapter": adapter, + }, + "displays": [ + { + "type": "LinearReferenceSequenceDisplay", + "displayId": "%s-LinearReferenceSequenceDisplay" % gname, + }, + { + "type": "LinearGCContentDisplay", + "displayId": "%s-LinearGCContentDisplay" % gname, + }, + ], + } + return trackDict + + def add_default_view(self): + cmd = [ + "jbrowse", + "set-default-session", + "-s", + self.config_json_file, + "-t", + ",".join(self.trackIdlist), + "-n", + "JBrowse2 in Galaxy", + "--target", + self.config_json_file, + "-v", + " LinearGenomeView", + ] + self.subprocess_check_call(cmd) + + def write_config(self): + with open(self.config_json_file, "w") as fp: + json.dump(self.config_json, fp, indent=2) + + def text_index(self): + # Index tracks + args = [ + "jbrowse", + "text-index", + "--target", + os.path.join(self.outdir, "data"), + "--assemblies", + self.genome_name, + ] + + tracks = ",".join(self.trackIdlist) + if tracks: + args += ["--tracks", tracks] + + self.subprocess_check_call(args) + + def add_hic(self, data, trackData): + """ + HiC adapter. + https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md + for testing locally, these work: + HiC data is from https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic + using hg19 reference track as a + 'BgzipFastaAdapter' + fastaLocation: + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz', + faiLocation: + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai', + gziLocation: + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', + Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438 + """ + tId = trackData["label"] + # can be served - if public. + # dsId = trackData["metadata"]["dataset_id"] + # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) + useuri = trackData["useuri"].lower() == "yes" + if useuri: + uri = data + else: + uri = trackData["hic_url"] + categ = trackData["category"] + trackDict = { + "type": "HicTrack", + "trackId": tId, + "name": uri, + "assemblyNames": [self.genome_name], + "category": [ + categ, + ], + "adapter": { + "type": "HicAdapter", + "hicLocation": uri, + }, + "displays": [ + { + "type": "LinearHicDisplay", + "displayId": "%s-LinearHicDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def add_maf(self, data, trackData): + """ + from https://github.com/cmdcolin/maf2bed + Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name + e.g. hg38.chr1 in the sequence identifiers. + need the reference id - eg hg18, for maf2bed.pl as the first parameter + """ + tId = trackData["label"] + mafPlugin = { + "plugins": [ + { + "name": "MafViewer", + "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js", + } + ] + } + categ = trackData["category"] + fname = "%s.bed" % tId + dest = "%s/%s" % (self.outdir, fname) + gname = self.genome_name + cmd = [ + "bash", + os.path.join(INSTALLED_TO, "convertMAF.sh"), + data, + gname, + INSTALLED_TO, + dest, + ] + self.subprocess_check_call(cmd) + # Construct samples list + # We could get this from galaxy metadata, not sure how easily. + ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE) + output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout) + ps.wait() + outp = output.decode("ascii") + soutp = outp.split("\n") + samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")] + samples = [x.split(".")[0] for x in samp] + trackDict = { + "type": "MafTrack", + "trackId": tId, + "name": trackData["name"], + "category": [ + categ, + ], + "adapter": { + "type": "MafTabixAdapter", + "samples": samples, + "bedGzLocation": { + "uri": fname + ".sorted.bed.gz", + }, + "index": { + "location": { + "uri": fname + ".sorted.bed.gz.tbi", + }, + }, + }, + "assemblyNames": [self.genome_name], + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % tId, + }, + { + "type": "LinearArcDisplay", + "displayId": "%s-LinearArcDisplay" % tId, + }, + ], + } + 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): + self.config_json["plugins"].append(mafPlugin[0]) + else: + self.config_json.update(mafPlugin) + + def _blastxml_to_gff3(self, xml, min_gap=10): + gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) + cmd = [ + "python", + os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"), + "--trim", + "--trim_end", + "--include_seq", + "--min_gap", + str(min_gap), + xml, + ] + subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) + gff3_unrebased.close() + return gff3_unrebased.name + + def add_blastxml(self, data, trackData, blastOpts, **kwargs): + gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"]) + + if "parent" in blastOpts and blastOpts["parent"] != "None": + gff3_rebased = tempfile.NamedTemporaryFile(delete=False) + cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")] + if blastOpts.get("protein", "false") == "true": + cmd.append("--protein2dna") + cmd.extend([os.path.realpath(blastOpts["parent"]), gff3]) + subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) + gff3_rebased.close() + + # Replace original gff3 file + shutil.copy(gff3_rebased.name, gff3) + os.unlink(gff3_rebased.name) + url = "%s.gff3" % trackData["label"] + dest = "%s/%s" % (self.outdir, url) + self._sort_gff(gff3, dest) + url = url + ".gz" + tId = trackData["label"] + categ = trackData["category"] + trackDict = { + "type": "FeatureTrack", + "trackId": tId, + "name": trackData["name"], + "assemblyNames": [self.genome_name], + "category": [ + categ, + ], + "adapter": { + "type": "Gff3TabixAdapter", + "gffGzLocation": { + "uri": url, + }, + "index": { + "location": { + "uri": url + ".tbi", + } + }, + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % tId, + }, + { + "type": "LinearArcDisplay", + "displayId": "%s-LinearArcDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + os.unlink(gff3) + + def add_bigwig(self, data, trackData): + """ "type": "LinearWiggleDisplay", + "configuration": {}, + "selectedRendering": "", + "resolution": 1, + "posColor": "rgb(228, 26, 28)", + "negColor": "rgb(255, 255, 51)", + "constraints": {} + """ + useuri = trackData["useuri"].lower() == "yes" + if useuri: + url = data + else: + url = "%s.bigwig" % trackData["label"] + # slashes in names cause path trouble + dest = os.path.join(self.outdir, url) + cmd = ["cp", data, dest] + self.subprocess_check_call(cmd) + bwloc = {"uri": url} + tId = trackData["label"] + categ = trackData["category"] + trackDict = { + "type": "QuantitativeTrack", + "trackId": tId, + "name": trackData["name"], + "category": [ + categ, + ], + "assemblyNames": [ + self.genome_name, + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": bwloc, + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "%s-LinearWiggleDisplay" % tId, + } + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def add_bam(self, data, trackData, bam_index=None, **kwargs): + tId = trackData["label"] + useuri = trackData["useuri"].lower() == "yes" + bindex = bam_index + categ = trackData["category"] + if useuri: + url = data + else: + fname = "%s.bam" % trackData["label"] + dest = "%s/%s" % (self.outdir, fname) + url = fname + bindex = fname + ".bai" + self.subprocess_check_call(["cp", data, dest]) + if bam_index is not None and os.path.exists(bam_index): + if not os.path.exists(bindex): + # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest + self.subprocess_check_call(["cp", bam_index, bindex]) + else: + # Can happen in exotic condition + # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam + # => no index generated by galaxy, but there might be one next to the symlink target + # this trick allows to skip the bam sorting made by galaxy if already done outside + if os.path.exists(os.path.realpath(data) + ".bai"): + self.symlink_or_copy(os.path.realpath(data) + ".bai", bindex) + else: + log.warn("Could not find a bam index (.bai file) for %s", data) + trackDict = { + "type": "AlignmentsTrack", + "trackId": tId, + "name": trackData["name"], + "category": [ + categ, + ], + "assemblyNames": [self.genome_name], + "adapter": { + "type": "BamAdapter", + "bamLocation": {"uri": url}, + "index": { + "location": { + "uri": bindex, + } + }, + }, + "displays": [ + { + "type": "LinearAlignmentsDisplay", + "displayId": "%s-LinearAlignmentsDisplay" % tId, + } + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def add_cram(self, data, trackData, cram_index=None, **kwargs): + tId = trackData["label"] + categ = trackData["category"] + useuri = trackData["useuri"].lower() == "yes" + if useuri: + url = data + else: + fname = "%s.cram" % trackData["label"] + dest = "%s/%s" % (self.outdir, fname) + url = fname + self.subprocess_check_call(["cp", data, dest]) + if cram_index is not None and os.path.exists(cram_index): + if not os.path.exists(dest + ".crai"): + # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest + self.subprocess_check_call( + ["cp", os.path.realpath(cram_index), dest + ".crai"] + ) + else: + cpath = os.path.realpath(dest) + ".crai" + cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)] + logging.debug("executing cmd %s" % " ".join(cmd)) + self.subprocess_check_call(cmd) + trackDict = { + "type": "AlignmentsTrack", + "trackId": tId, + "name": trackData["name"], + "category": [ + categ, + ], + "assemblyNames": [self.genome_name], + "adapter": { + "type": "CramAdapter", + "cramLocation": {"uri": url}, + "craiLocation": { + "uri": url + ".crai", + }, + "sequenceAdapter": self.genome_sequence_adapter, + }, + "displays": [ + { + "type": "LinearAlignmentsDisplay", + "displayId": "%s-LinearAlignmentsDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def add_vcf(self, data, trackData): + tId = trackData["label"] + # url = "%s/api/datasets/%s/display" % ( + # self.giURL, + # trackData["metadata"]["dataset_id"], + # ) + categ = trackData["category"] + useuri = trackData["useuri"].lower() == "yes" + if useuri: + url = data + else: + url = "%s.vcf.gz" % tId + dest = "%s/%s" % (self.outdir, url) + cmd = "bgzip -c %s > %s" % (data, dest) + self.subprocess_popen(cmd) + cmd = ["tabix", "-f", "-p", "vcf", dest] + self.subprocess_check_call(cmd) + trackDict = { + "type": "VariantTrack", + "trackId": tId, + "name": trackData["name"], + "assemblyNames": [self.genome_name], + "category": [ + categ, + ], + "adapter": { + "type": "VcfTabixAdapter", + "vcfGzLocation": {"uri": url}, + "index": { + "location": { + "uri": url + ".tbi", + } + }, + }, + "displays": [ + { + "type": "LinearVariantDisplay", + "displayId": "%s-LinearVariantDisplay" % tId, + }, + { + "type": "ChordVariantDisplay", + "displayId": "%s-ChordVariantDisplay" % tId, + }, + { + "type": "LinearPairedArcDisplay", + "displayId": "%s-LinearPairedArcDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def _sort_gff(self, data, dest): + # Only index if not already done + if not os.path.exists(dest): + cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % ( + data, + dest, + ) # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" + self.subprocess_popen(cmd) + self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest]) + + def _sort_bed(self, data, dest): + # Only index if not already done + if not os.path.exists(dest): + cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest) + self.subprocess_popen(cmd) + cmd = ["tabix", "-f", "-p", "bed", dest] + self.subprocess_check_call(cmd) + + def add_gff(self, data, ext, trackData): + useuri = trackData["useuri"].lower() == "yes" + if useuri: + url = trackData["path"] + else: + url = "%s.%s.gz" % (trackData["label"], ext) + dest = "%s/%s" % (self.outdir, url) + self._sort_gff(data, dest) + tId = trackData["label"] + categ = trackData["category"] + trackDict = { + "type": "FeatureTrack", + "trackId": tId, + "name": trackData["name"], + "assemblyNames": [self.genome_name], + "category": [ + categ, + ], + "adapter": { + "type": "Gff3TabixAdapter", + "gffGzLocation": { + "uri": url, + }, + "index": { + "location": { + "uri": url + ".tbi", + } + }, + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % tId, + }, + { + "type": "LinearArcDisplay", + "displayId": "%s-LinearArcDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def add_bed(self, data, ext, trackData): + tId = trackData["label"] + categ = trackData["category"] + useuri = trackData["useuri"].lower() == "yes" + if useuri: + url = data + else: + url = "%s.%s.gz" % (trackData["label"], ext) + dest = "%s/%s" % (self.outdir, url) + self._sort_bed(data, dest) + trackDict = { + "type": "FeatureTrack", + "trackId": tId, + "name": trackData["name"], + "assemblyNames": [self.genome_name], + "adapter": { + "category": [ + categ, + ], + "type": "BedTabixAdapter", + "bedGzLocation": { + "uri": url, + }, + "index": { + "location": { + "uri": url + ".tbi", + } + }, + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % tId, + }, + { + "type": "LinearPileupDisplay", + "displayId": "%s-LinearPileupDisplay" % tId, + }, + { + "type": "LinearArcDisplay", + "displayId": "%s-LinearArcDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def add_paf(self, data, trackData, pafOpts, **kwargs): + 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(",")] + passnames = [self.genome_name] # always first + 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, + ] + url = "%s.paf" % (trackData["label"]) + dest = "%s/%s" % (self.outdir, url) + self.symlink_or_copy(os.path.realpath(data), dest) + trackDict = { + "type": "SyntenyTrack", + "trackId": tId, + "assemblyNames": passnames, + "category": [ + categ, + ], + "name": tname, + "adapter": { + "type": "PAFAdapter", + "pafLocation": {"uri": url}, + "assemblyNames": passnames, + }, + "displays": [ + { + "type": "LinearSyntenyDisplay", + "displayId": "%s-LinearSyntenyDisplay" % tId, + }, + { + "type": "DotPlotDisplay", + "displayId": "%s-DotPlotDisplay" % tId, + }, + ], + } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json + self.tracksToAdd.append(trackDict) + self.trackIdlist.append(tId) + + def process_annotations(self, track): + category = track["category"].replace("__pd__date__pd__", TODAY) + for i, ( + dataset_path, + dataset_ext, + useuri, + track_human_label, + extra_metadata, + ) in enumerate(track["trackfiles"]): + if not dataset_path.strip().startswith("http"): + # Unsanitize labels (element_identifiers are always sanitized by Galaxy) + for key, value in mapped_chars.items(): + track_human_label = track_human_label.replace(value, key) + track_human_label = track_human_label.replace(" ", "_") + outputTrackConfig = { + "category": category, + "style": track["style"], + } + + outputTrackConfig["label"] = "%s_%i_%s" % ( + dataset_ext, + i, + track_human_label, + ) + outputTrackConfig["useuri"] = useuri + outputTrackConfig["path"] = dataset_path + outputTrackConfig["ext"] = dataset_ext + outputTrackConfig["key"] = track_human_label + + outputTrackConfig["trackset"] = track.get("trackset", {}) + outputTrackConfig["metadata"] = extra_metadata + outputTrackConfig["name"] = track_human_label + + if dataset_ext in ("gff", "gff3"): + self.add_gff( + dataset_path, + dataset_ext, + outputTrackConfig, + ) + elif dataset_ext in ("hic", "juicebox_hic"): + self.add_hic( + dataset_path, + outputTrackConfig, + ) + elif dataset_ext in ("cool", "mcool", "scool"): + hic_url = "%s_%d.juicebox_hic" % (track_human_label, i) + hic_path = os.path.join(self.outdir, hic_url) + self.subprocess_check_call( + [ + "hictk", + "convert", + "-f", + "--output-fmt", + "hic", + dataset_path, + hic_path, + ] + ) + outputTrackConfig["hic_url"] = hic_url + self.add_hic( + hic_path, + outputTrackConfig, + ) + elif dataset_ext in ("bed",): + self.add_bed( + dataset_path, + dataset_ext, + outputTrackConfig, + ) + elif dataset_ext in ("maf",): + self.add_maf( + dataset_path, + outputTrackConfig, + ) + elif dataset_ext == "bigwig": + self.add_bigwig( + dataset_path, + outputTrackConfig, + ) + elif dataset_ext == "bam": + real_indexes = track["conf"]["options"]["bam"]["bam_index"] + self.add_bam( + dataset_path, + outputTrackConfig, + bam_index=real_indexes, + ) + elif dataset_ext == "cram": + real_indexes = track["conf"]["options"]["cram"]["cram_index"] + self.add_cram( + dataset_path, + outputTrackConfig, + cram_index=real_indexes, + ) + elif dataset_ext == "blastxml": + self.add_blastxml( + dataset_path, + outputTrackConfig, + track["conf"]["options"]["blast"], + ) + elif dataset_ext == "vcf": + self.add_vcf(dataset_path, outputTrackConfig) + elif dataset_ext == "paf": + self.add_paf( + dataset_path, + outputTrackConfig, + track["conf"]["options"]["paf"], + ) + else: + logging.warn("Do not know how to handle %s", dataset_ext) + # Return non-human label for use in other fields + yield outputTrackConfig["label"] + + def add_default_session(self, default_data): + """ + Add some default session settings: set some assemblies/tracks on/off + + labels off 1 + { + "id": "JJNRSOoj8cPCTR8ZJ7Yne", + "type": "VariantTrack", + "configuration": "vcf_0_merlin.vcf", + "minimized": false, + "displays": [ + { + "id": "JOvAkv1bdyz5SAJs3JBby", + "type": "LinearVariantDisplay", + "configuration": {}, + "trackShowLabels": false, + "trackShowDescriptions": false + } + ] + }, + + track labels at end of default view + "hideHeader": false, + "hideHeaderOverview": false, + "hideNoTracksActive": false, + "trackSelectorType": "hierarchical", + "showCenterLine": false, + "showCytobandsSetting": true, + "trackLabels": "hidden", + "showGridlines": true, + "showBookmarkHighlights": true, + "showBookmarkLabels": true + } + ], + "sessionTracks": [], + "sessionAssemblies": [], + "temporaryAssemblies": [], + "connectionInstances": [], + "sessionConnections": [], + "focusedViewId": "n-7YuEPiR5QUtHntU-xcO", + "sessionPlugins": [] + } + } + + + """ + tracks_data = [] + + # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 + + # We need to know the track type from the config.json generated just before + track_types = {} + with open(self.config_json_file, "r") as config_file: + config_json = json.load(config_file) + if self.config_json: + config_json.update(self.config_json) + + for track_conf in self.tracksToAdd: + tId = track_conf["trackId"] + track_types[tId] = track_conf["type"] + style_data = default_data["style"][tId] + logging.warn( + "### defsession for %s got style_data=%s given default_data %s" + % (tId, style_data, default_data) + ) + 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? + style_data["labels"] = track_conf["style_labels"] + tracks_data.append( + { + "type": track_types[tId], + "configuration": tId, + "displays": [style_data], + } + ) + + # The view for the assembly we're adding + view_json = {"type": "LinearGenomeView", "tracks": tracks_data} + + refName = None + drdict = { + "reversed": False, + "assemblyName": self.genome_name, + "start": 1, + "end": 200000, + "refName": "x", + } + + if default_data.get("defaultLocation", ""): + ddl = default_data["defaultLocation"] + 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 + ) + else: + drdict["refName"] = self.genome_firstcontig + 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_name = default_data.get("session_name", "New session") + for key, value in mapped_chars.items(): + session_name = session_name.replace(value, key) + # Merge with possibly existing defaultSession (if upgrading a jbrowse instance) + session_json = {} + if "defaultSession" in config_json: + session_json = config_json["defaultSession"] + + session_json["name"] = session_name + + if "views" not in session_json: + session_json["views"] = [] + + session_json["views"].append(view_json) + + config_json["defaultSession"] = session_json + self.config_json.update(config_json) + + with open(self.config_json_file, "w") as config_file: + json.dump(self.config_json, config_file, indent=2) + + def add_general_configuration(self, data): + """ + Add some general configuration to the config.json file + """ + + config_path = self.config_json_file + if os.path.exists(config_path): + with open(config_path, "r") as config_file: + config_json = json.load(config_file) + else: + config_json = {} + if self.config_json: + config_json.update(self.config_json) + config_data = {} + + config_data["disableAnalytics"] = data.get("analytics", "false") == "true" + + config_data["theme"] = { + "palette": { + "primary": {"main": data.get("primary_color", "#0D233F")}, + "secondary": {"main": data.get("secondary_color", "#721E63")}, + "tertiary": {"main": data.get("tertiary_color", "#135560")}, + "quaternary": {"main": data.get("quaternary_color", "#FFB11D")}, + }, + "typography": {"fontSize": int(data.get("font_size", 10))}, + } + if not config_json.get("configuration", None): + config_json["configuration"] = {} + config_json["configuration"].update(config_data) + self.config_json.update(config_json) + with open(config_path, "w") as config_file: + json.dump(self.config_json, config_file, indent=2) + + def clone_jbrowse(self, realclone=True): + """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now""" + dest = self.outdir + if realclone: + self.subprocess_check_call( + ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"] + ) + else: + shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True) + for fn in [ + "asset-manifest.json", + "favicon.ico", + "robots.txt", + "umd_plugin.js", + "version.txt", + "test_data", + ]: + cmd = ["rm", "-rf", os.path.join(dest, fn)] + self.subprocess_check_call(cmd) + cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest] + self.subprocess_check_call(cmd) + + +def parse_style_conf(item): + if "type" in item.attrib and item.attrib["type"] in [ + "boolean", + "integer", + ]: + if item.attrib["type"] == "boolean": + return item.text in ("yes", "true", "True") + elif item.attrib["type"] == "integer": + return int(item.text) + else: + return item.text + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="", epilog="") + parser.add_argument("--xml", help="Track Configuration") + parser.add_argument( + "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda" + ) + parser.add_argument("--outdir", help="Output directory", default="out") + parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1") + args = parser.parse_args() + tree = ET.parse(args.xml) + root = tree.getroot() + + # This should be done ASAP + GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text + # Sometimes this comes as `localhost` without a protocol + if not GALAXY_INFRASTRUCTURE_URL.startswith("http"): + # so we'll prepend `http://` and hope for the best. Requests *should* + # be GET and not POST so it should redirect OK + GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL + jc = JbrowseConnector( + outdir=args.outdir, + jbrowse2path=args.jbrowse2path, + genomes=[ + { + "path": x.attrib["path"], + "label": x.attrib["label"], + "useuri": x.attrib["useuri"], + "meta": metadata_from_node(x.find("metadata")), + } + for x in root.findall("metadata/genomes/genome") + ], + ) + jc.process_genomes() + + # .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py + default_session_data = { + "visibility": { + "default_on": [], + "default_off": [], + }, + "style": {}, + "style_labels": {}, + } + for track in root.findall("tracks/track"): + track_conf = {} + track_conf["trackfiles"] = [] + + is_multi_bigwig = False + try: + if track.find("options/wiggle/multibigwig") and ( + track.find("options/wiggle/multibigwig").text == "True" + ): + is_multi_bigwig = True + multi_bigwig_paths = [] + except KeyError: + pass + + trackfiles = track.findall("files/trackFile") + if trackfiles: + for x in track.findall("files/trackFile"): + track_conf["label"] = x.attrib["label"] + track_conf["useuri"] = x.attrib["useuri"] + if is_multi_bigwig: + multi_bigwig_paths.append( + ( + x.attrib["label"], + x.attrib["useuri"], + os.path.realpath(x.attrib["path"]), + ) + ) + else: + if trackfiles: + metadata = metadata_from_node(x.find("metadata")) + track_conf["dataset_id"] = metadata["dataset_id"] + if x.attrib["useuri"].lower() == "yes": + tfa = ( + x.attrib["path"], + x.attrib["ext"], + x.attrib["useuri"], + x.attrib["label"], + metadata, + ) + else: + tfa = ( + os.path.realpath(x.attrib["path"]), + x.attrib["ext"], + x.attrib["useuri"], + x.attrib["label"], + metadata, + ) + track_conf["trackfiles"].append(tfa) + + if is_multi_bigwig: + metadata = metadata_from_node(x.find("metadata")) + + track_conf["trackfiles"].append( + ( + multi_bigwig_paths, # Passing an array of paths to represent as one track + "bigwig_multiple", + "MultiBigWig", # Giving an hardcoded name for now + {}, # No metadata for multiple bigwig + ) + ) + track_conf["category"] = track.attrib["cat"] + track_conf["format"] = track.attrib["format"] + if track.find("options/style"): + track_conf["style"] = { + item.tag: parse_style_conf(item) for item in track.find("options/style") + } + else: + track_conf["style"] = {} + tst = track_conf["style"].get("type", None) + if tst: + track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst) + logging.warn("### got %s for track style" % track_conf["style"]) + if track.find("options/style_labels"): + track_conf["style_labels"] = { + item.tag: parse_style_conf(item) + for item in track.find("options/style_labels") + } + track_conf["conf"] = etree_to_dict(track.find("options")) + track_conf["category"] = track.attrib["cat"] + track_conf["format"] = track.attrib["format"] + keys = jc.process_annotations(track_conf) + + if keys: + for key in keys: + default_session_data["visibility"][ + track.attrib.get("visibility", "default_off") + ].append(key) + if track_conf.get("style", None): + default_session_data["style"][key] = track_conf["style"] + if track_conf.get("style_labels", None): + default_session_data["style_labels"][key] = track_conf.get( + "style_labels", None + ) + logging.warn( + "# after process, key=%s def session style = %s" + % (key, default_session_data["style"][key]) + ) + default_session_data["defaultLocation"] = root.find( + "metadata/general/defaultLocation" + ).text + default_session_data["session_name"] = root.find( + "metadata/general/session_name" + ).text + jc.zipOut = root.find("metadata/general/zipOut").text == "true" + general_data = { + "analytics": root.find("metadata/general/analytics").text, + "primary_color": root.find("metadata/general/primary_color").text, + "secondary_color": root.find("metadata/general/secondary_color").text, + "tertiary_color": root.find("metadata/general/tertiary_color").text, + "quaternary_color": root.find("metadata/general/quaternary_color").text, + "font_size": root.find("metadata/general/font_size").text, + } + jc.add_general_configuration(general_data) + trackconf = jc.config_json.get("tracks", None) + if trackconf: + jc.config_json["tracks"].update(jc.tracksToAdd) + else: + jc.config_json["tracks"] = jc.tracksToAdd + jc.write_config() + jc.add_default_session(default_session_data) + logging.warn("### got default_session_data=%s" % default_session_data) + # jc.text_index() not sure what broke here.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse2broken.xml Thu Mar 21 08:01:42 2024 +0000 @@ -0,0 +1,961 @@ + <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_7" profile="22.05"> + <description>genome browser</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edamInc"/> + <xrefs> + <xref type="bio.tools">jbrowse2</xref> + </xrefs> + <expand macro="requirements"/> + <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> + <command detect_errors="aggressive"><![CDATA[ +mkdir -p '$output.files_path' && +## Copy the XML file into the directory, mostly for debugging +## but nice if users want to reproduce locally +cp '$trackxml' '$output.files_path/galaxy.xml' && + +export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && + +#if $jbgen.ucol.formcoll=="collect": + python '$__tool_directory__/autogenJB2.py' + #for $key in $autoCollection.keys(): + #if $autoCollection[$key].is_collection: + #set subCol=$autoCollection[$key] + #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf'] + #if len($pafs) > 0: + --pafmeta '$pafs[0]' + #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta'] + #for $ref in $refs: + --pafreferencemeta '$ref' + #end for + #end if + #else if $autoCollection[$key].ext == 'fasta': + --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key' + #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf'] + --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key' + #else if $autoCollection[$key].ext in ['bam',] + --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index' + #else if $autoCollection[$key].ext in ['cram',] + --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index' + #end if + #end for + --outdir '$output.files_path' + --jbrowse2path \${JBROWSE2_PATH} + --sessName "Autogen JBrowse" && + #if $jbgen.zipOut == "true": + (cd '$output.files_path' && zip -r - . ) > '$output' + #else + cp '$output.files_path/index.html' '$output' + #end if +#else: + python '$__tool_directory__/jbrowse2.py' + --jbrowse2path \${JBROWSE2_PATH} + --outdir '$output.files_path' + --xml '$trackxml' && + #if $jbgen.zipOut == "true": + (cd '$output.files_path' && zip -r - . ) > '$output' + #else + cp '$output.files_path/index.html' '$output' + #end if + ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. + #if str($uglyTestingHack) == "enabled": + && cp '$trackxml' '$output' + #end if +#end if + ]]></command> +<configfiles> + <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> +#if $jbgen.ucol.formcoll=="form": +<root> + <metadata> + <genomes> + #if str($reference_genome.genome_type_select) == "uri": + <genome path="${reference_genome.uri}" label="${reference_genome.refname}" useuri="yes"> + <metadata> + <dataset + dname = "${reference_genome.refname}" /> + </metadata> + </genome> + #else if str($reference_genome.genome_type_select) == "indexed": + <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no"> + <metadata> + <dataset + dname = "${reference_genome.genome.fields.name}" /> + </metadata> + </genome> + #else + <genome path="$reference_genome.genome" label="${reference_genome.genome.name}" useuri="no"> + <metadata> + <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" + size="${reference_genome.genome.get_size(nice_size=True)}" + edam_format="${reference_genome.genome.datatype.edam_format}" + file_ext="${reference_genome.genome.ext}" + dname = "${reference_genome.genome.name}" /> + <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}" + #if $reference_genome.genome.history.user: + user_email="${reference_genome.genome.history.user.email}" + user_id="${reference_genome.genome.history.user_id}" + display_name="${reference_genome.genome.history.get_display_name()}"/> + #else + user_email="anonymous" + user_id="-1" + display_name="Unnamed History"/> + #end if + <metadata + #for (key, value) in $reference_genome.genome.get_metadata().items(): + #if "_types" not in $key: + #if isinstance($value, list): + #set value_str = "[%s]" % ','.join([str(val) for val in value]) + ${key}="$value_str" + #else + ${key}="${value}" + #end if + #end if + #end for + /> + <tool + tool_id="${reference_genome.genome.creating_job.tool_id}" + tool_version="${reference_genome.genome.creating_job.tool_version}" + /> + </metadata> + </genome> + #end if + </genomes> + <general> + <defaultLocation>${jbgen.defaultLocation}</defaultLocation> + <zipOut>${jbgen.zipOut}</zipOut> + <analytics>${jbgen.enableAnalytics}</analytics> + <primary_color>${jbgen.primary_color}</primary_color> + <secondary_color>${jbgen.secondary_color}</secondary_color> + <tertiary_color>${jbgen.tertiary_color}</tertiary_color> + <quaternary_color>${jbgen.quaternary_color}</quaternary_color> + <font_size>${jbgen.font_size}</font_size> + <session_name>${jbgen.session_name}</session_name> + </general> + <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> + </metadata> + <tracks> + #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> + #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}"> + <files> + #for $dataset in $track.data_format.useuri.annotation: + <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> + <metadata> + + <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" + size="${dataset.get_size(nice_size=True)}" + edam_format="${dataset.datatype.edam_format}" + file_ext="${dataset.ext}" /> + <history id="${__app__.security.encode_id($dataset.history_id)}" + #if $dataset.history.user: + user_email="${dataset.history.user.email}" + user_id="${dataset.history.user_id}" + display_name="${dataset.history.get_display_name()}"/> + #else + user_email="anonymous" + user_id="-1" + display_name="Unnamed History"/> + #end if + + <metadata + #for (key, value) in $dataset.get_metadata().items(): + #if "_types" not in $key and $value is not None and len(str($value)) < 5000: + #if isinstance($value, list): + #set value_str = "[%s]" % ','.join([str(val) for val in value]) + ${key}="$value_str" + #else + ${key}="${value}" + #end if + #end if + #end for + /> + <tool + tool_id="${dataset.creating_job.tool_id}" + tool_version="${dataset.creating_job.tool_version}" + /> + </metadata> + </trackFile> + #end for + </files> + + <options> + <style> + #if str($track.data_format.data_format_select) in ["gff", "bed", "paf", "blastxml"]: + <type>${track.data_format.jbstyle.track_style.display}</type> + #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay"]: + <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> + <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> + #end if + #end if + #if str($track.data_format.data_format_select) in ["bam", "cram"]: + <type>"LinearAlignmentsDisplay"</type> + #end if + </style> + #if str($track.data_format.data_format_select) == "bam": + <bam> + #for $dataset in $track.data_format.useuri.annotation: + <bam_index>${dataset.metadata.bam_index}</bam_index> + #end for + </bam> + #else if str($track.data_format.data_format_select) == "cram": + <cram> + #for $dataset in $track.data_format.useuri.annotation: + <cram_index>${dataset.metadata.cram_index}</cram_index> + #end for + </cram> + #else if str($track.data_format.data_format_select) == "blastxml": + <blast> + #if str($track.data_format.blast_parent) != "": + <parent>${track.data_format.blast_parent}</parent> + #end if + <protein>${track.data_format.is_protein}</protein> + <min_gap>${track.data_format.min_gap}</min_gap> + </blast> + #else if str($track.data_format.data_format_select) == "gff": + <gff> + #if $track.data_format.match_part.match_part_select == "true": + <match>${track.data_format.match_part.name}</match> + #end if + </gff> + #else if str($track.data_format.data_format_select) == "paf": + <paf> + <genome> + #for gnome in $track.data_format.synteny_genome: + $gnome, + #end for + </genome> + <genome_label> + #for gnome in $track.data_format.synteny_genome: + $gnome.name, + #end for + </genome_label> + </paf> + #else if str($track.data_format.data_format_select) == "hic": + <hic> + </hic> + #else if str($track.data_format.data_format_select) == "cool": + <cool> + </cool> + #else if str($track.data_format.data_format_select) == "bed": + <bed> + </bed> + #else if str($track.data_format.data_format_select) == "sparql": + <label>${track.data_format.label}</label> + <sparql> + <url>${track.data_format.url}</url> + <query>${track.data_format.query}</query> + <query_refnames>${track.data_format.query_refnames}</query_refnames> + </sparql> + #end if + </options> + </track> + #end if + #end if + #end for + #end for + </tracks> +</root> +#end if +]]></configfile> + </configfiles> + + <inputs> + <conditional name="reference_genome"> + <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> + <option selected="True" value="indexed">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + <option value="uri">URI for a reference in tabix .gz format </option> + </param> + <when value="indexed"> + <param + help="If your genome of interest is not listed, contact the Galaxy team" + label="Select a reference genome" + name="genome" + type="select" + optional="true"> + <options from_data_table="all_fasta"> + <filter column="2" type="sort_by"/> + <validator message="No genomes are available for the selected input dataset" type="no_options"> + </validator> + </options> + </param> + </when> + <when value="history"> + <param + format="fasta" + label="Select the reference genome" + name="genome" + type="data" + optional="true"> + </param> + </when> + <when value="uri"> + <param + label="URI pointing to tabix compressed fasta" + name="uri" + type="text"> + </param> + <param + label="Reference key - dbkey equivalent" + name="refname" + type="text"> + </param> + </when> + </conditional> + + <repeat name="track_groups" title="Track Group"> + <param label="Track Category" + name="category" + type="text" + value="Default" + help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/> + <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="bed">BED track</option> + <option value="bigwig">BigWig track</option> + <option value="blastxml">Blast XML track - converted to GFF</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> + </param> + <when value="blastxml"> + <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> + + <param label="Features used in Blast Search" + help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this." + format="gff3" + name="blast_parent" + optional="true" + type="data"/> + + <param label="Minimum Gap Size" + help="before a new match_part feature is created" + name="min_gap" + type="integer" + value="10" + min="2" /> + <param label="Is this a protein blast search?" + type="boolean" + name="is_protein" + truevalue="true" + falsevalue="false" /> + <expand macro="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + <when value="vcf"> + <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" /> + <expand macro="track_styling_vcf"/> + <expand macro="track_visibility" /> + </when> + <when value="gff"> + <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3" /> + <conditional name="match_part" label="match/match_part data"> + <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select"> + <option selected="True" value="false">Not match/match part data</option> + <option value="true">Match/match part data</option> + </param> + <when value="true"> + <param label="Match Part Feature Type" + name="name" + type="text" + value="match" + help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)." + optional="True"/> + </when> + <when value="false" /> + </conditional> + <expand macro="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + <when value="bam"> + <expand macro="input_conditional" label="BAM Track Data" format="bam" /> + <expand macro="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + <when value="bed"> + <expand macro="input_conditional" label="BED Track Data" format="bed" /> + <expand macro="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + <when value="cram"> + <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> + <expand macro="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + <when value="maf"> + <expand macro="input_conditional" label="MAF Track Data" format="maf" /> + <expand macro="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + <when value="bigwig"> + <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> + <expand macro="track_styling_bigwig" /> + <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="track_styling_feature" /> + <expand macro="track_visibility" /> + </when> + + <when value="hic"> + <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" /> + <expand macro="track_visibility" /> + </when> + <when value="cool"> + <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" /> + <expand macro="track_visibility" /> + </when> + </conditional> + </repeat> + </repeat> + + <expand macro="general_options" /> + + <param type="hidden" name="uglyTestingHack" value="" /> + </inputs> + <outputs> + <data format="html" name="output" label="JBrowse2"> + <change_format> + <when input="zipOut" value="true" format="zip" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="bigwig"/> + <conditional name="useuri"> + <param name="annotation" value="bw/merlin.bw"/> + <param name="insource" value="history"/> + </conditional> + </conditional> + </repeat> + </repeat> + <param name="uglyTestingHack" value="enabled" /> + <output name="output"> + <assert_contents> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + <has_text text="trackFile path="></has_text> + <has_text text="file_ext="bigwig""></has_text> + <has_text text="format="bigwig""></has_text> + </assert_contents> + </output> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="vcf"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="vcf/merlin.vcf"/> + </conditional> + </conditional> + </repeat> + </repeat> + <param name="uglyTestingHack" value="enabled" /> + <output name="output"> + <assert_contents> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + <has_text text="trackFile path="></has_text> + <has_text text="ext="vcf" label="merlin.vcf""></has_text> + </assert_contents> + </output> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <param name="uglyTestingHack" value="enabled" /> + <output name="output"> + <assert_contents> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + </assert_contents> + </output> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="bed"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="bed/test-3.bed"/> + </conditional> + </conditional> + </repeat> + </repeat> + <param name="uglyTestingHack" value="enabled" /> + <output name="output"> + <assert_contents> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + <has_text text="trackFile path="></has_text> + <has_text text="ext="bed" label="test-3.bed""></has_text> + </assert_contents> + </output> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <repeat name="track_groups"> + <param name="category" value="Auto Coloured" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="gff3/A.gff"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + </conditional> + </repeat> + </repeat> + + <repeat name="track_groups"> + <param name="category" value="Ignore Scale" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="gff3/1.gff"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + <conditional name="color"> + <param name="color_select" value="manual"/> + <param name="style_color" value="#ff00ff"/> + </conditional> + </conditional> + </section> + </conditional> + </repeat> + </repeat> + + <repeat name="track_groups"> + <param name="category" value="Scaled Colour" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="insource" value= "history"/> + <param name="annotation" value="gff3/C.gff"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="automatic"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </conditional> + </conditional> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/B.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="automatic"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="manual"/> + <param name="style_color" value="#0000ff"/> + </conditional> + </conditional> + </conditional> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/A.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="manual"/> + <param name="minimum" value="0"/> + <param name="maximum" value="1000"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </conditional> + </conditional> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/1.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="manual"/> + <param name="minimum" value="0"/> + <param name="maximum" value="1000"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="manual"/> + <param name="style_color" value="#ff0000"/> + </conditional> + </conditional> + </conditional> + </section> + </conditional> + </repeat> + </repeat> + + <repeat name="track_groups"> + <param name="category" value="Realistic" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/interpro.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/2.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="true"/> + <param name="name" value="cDNA_match"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + </conditional> + </repeat> + </repeat> + + <param name="uglyTestingHack" value="enabled" /> + <output name="output"> + <assert_contents> + <has_text text="Auto Coloured"/> + <has_text text="A.gff"/> + <has_text text="B.gff"/> + <has_text text="C.gff"/> + <has_text text="interpro.gff"/> + <has_text text="Scaled Colour"/> + <has_text text="1.gff"/> + <has_text text="2.gff"/> + </assert_contents> + </output> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + + <repeat name="track_groups"> + <param name="category" value="With menu or index" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/1.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + <section name="jbmenu"> + <repeat name="track_menu"> + <param name="menu_action" value="iframeDialog"/> + <param name="menu_label" value="Some menu item"/> + <param name="menu_title" value="Frame title"/> + <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> + <param name="menu_icon" value="dijitIconNewTask"/> + </repeat> + <repeat name="track_menu"> + <param name="menu_action" value="newWindow"/> + <param name="menu_label" value="Another menu item"/> + <param name="menu_title" value="Frame title 2"/> + <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> + </repeat> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/1.gff"/> + <param name="insource" value= "history"/> + </conditional> + <param name="insource" value= "history"/> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + </conditional> + </repeat> + </repeat> + + <param name="uglyTestingHack" value="enabled" /> + <output name="output"> + <assert_contents> + <has_text text="With menu or index"/> + <has_text text="gff"/> + </assert_contents> + </output> + </test> + <!-- TODO add a synteny test --> + <!-- TODO add a bam and a cram test --> + <!-- TODO add an hic test --> + <!-- TODO add a vcf_bgzip test --> + </tests> + <help><![CDATA[ + +JBrowse2-in-Galaxy +================== + +JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible +alternative to JBrowse1-in-Galaxy and Trackster. + +Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes, +and detailed track styling is not yet implemented. Send code. +JBrowse1 development has now ceased in favour of JBrowse2. + +Use and local viewing +===================== + + +A JBrowse2 history item can be opened by viewing it (the "eye" icon). + +The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history. +This can be shared and viewed without Galaxy. + +A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive, +assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change +directory to the first level in that zip archive. It contains a file named *jb2_webserver.py* + +With python3 installed, + +*python3 jb2_webserver.py* + +will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open, +but the script appears to be running, try pointing your web browser to the default of *localhost:8080* + +Overview +-------- + +JBrowse is a fast, embeddable genome browser built completely with +JavaScript and HTML5. + +The JBrowse-in-Galaxy (JiG) tool was written to help build complex +JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying +about how to run the command line tools to format your data, and which +options need to be supplied and where. + +Options +------- + +**Reference or Assembly** + +Choose either a built-in or select one from your history. + +Track coordinates and contig names *must* match this reference precisely +or they will not display. + +**Track Groups** represent a set of tracks in a single category. + +Annotation Tracks +----------------- + +GFF3/BED +~~~~~~~~ + +Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region. + +When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads +to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is +selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works +well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the +lengths of each assembly or reference contig. + +BAM Pileups +~~~~~~~~~~~ + +We support BAM files and can automatically generate SNP tracks based on +that bam data. + + +BlastXML +~~~~~~~~ + +JiG now supports both blastn and blastp datasets. JiG internally uses a +blastXML to gapped GFF3 tool to convert your blastxml datasets into a +format amenable to visualization in JBrowse. This tool is also +available separately from the IUC on the toolshed. + +**Minimum Gap Size** reflects how long a gap must be before it becomes a +real gap in the processed gff3 file. In the picture above, various sizes +of gaps can be seen. If the minimum gap size was set much higher, say +100nt, many of the smaller gaps would disappear, and the features on +both sides would be merged into one, longer feature. This setting is +inversely proportional to runtime and output file size. *Do not set this +to a low value for large datasets*. By setting this number lower, you +will have extremely large outputs and extremely long runtimes. The +default was configured based off of the author's experience, but the +author only works on small viruses. It is *strongly* recommended that +you filter your blast results before display, e.g. picking out the top +10 hits or so. + +**Protein blast search** option merely informs underlying tools that +they should adjust feature locations by 3x. + + +@ATTRIBUTION@ +]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macrosbroken.xml Thu Mar 21 08:01:42 2024 +0000 @@ -0,0 +1,548 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.10.1</token> + <xml name = "edamInc"> + <edam_topics> + <edam_topic>topic_3307</edam_topic> + <edam_topic>topic_0092</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0573</edam_operation> + <edam_operation>operation_0564</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> + <requirement type="package" version="1.81">biopython</requirement> + <requirement type="package" version="0.7.1">bcbio-gff</requirement> + <requirement type="package" version="1.19">samtools</requirement> + <requirement type="package" version="6.0.1">pyyaml</requirement> + <requirement type="package" version="1.11">tabix</requirement> + <requirement type="package" version="4.6.0">findutils</requirement> + <requirement type="package" version="0.0.8">hictk</requirement> + <yield/> + </requirements> + </xml> + <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> + <token name="@WRAPPER_VERSION@">galaxy2</token> + <token name="@ATTRIBUTION@"><![CDATA[ +**Attribution** +This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is maintained by Ross Lazarus +until the IUC complete their own. +]]> + </token> + <xml name="genome_selector" + token_help="" + token_label="Fasta sequences" + token_optional="False" > + <conditional name="reference_genome"> + <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> + <option selected="True" value="indexed">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="indexed"> + <param + help="@HELP@" + label="@LABEL@" + name="genomes" + type="select" + optional="@OPTIONAL@" + > + <options from_data_table="all_fasta"> + <filter column="2" type="sort_by" /> + <validator message="No genomes are available for the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param + format="fasta" + label="@LABEL@" + help="@HELP@" + name="genomes" + type="data" + optional="@OPTIONAL@" + multiple="True" /> + </when> + </conditional> + </xml> + + <xml name="auto_manual_tk" + token_cond_label="Color" + token_cond_name="color" + token_select_label="Color Specification" + token_select_name="color_select" + token_automatic_label="Automatically selected" + token_manual_label="Manual Color Selection"> + <conditional name="@COND_NAME@" label="@COND_LABEL@"> + <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@"> + <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> + <option value="manual">@MANUAL_LABEL@</option> + </param> + <when value="automatic"> + </when> + <when value="manual"> + <yield /> + </when> + </conditional> + </xml> + + <xml name="jb_color" + token_label="JBrowse style.color" + token_name="style_color" + token_value="goldenrod" + token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS" + > + <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + </xml> + + <xml name="auto_color" + token_cond_label="Color" + token_cond_name="color" + token_select_label="Color Selection" + token_select_name="color_select" + token_automatic_label="Automatically selected" + token_manual_label="Manual Color Selection"> + <expand macro="auto_manual_tk" + cond_label="@COND_LABEL@" + cond_name="@COND_NAME@" + select_label="@SELECT_LABEL@" + select_name="@SELECT_NAME@" + automatic_label="@AUTOMATIC_LABEL@" + manual_label="@MANUAL_LABEL@"> + <expand macro="jb_color" /> + <yield /> + </expand> + </xml> + + + + <xml name="brewer_scheme"> + <param type="select" label="Brewer color Scheme" name="brewer_scheme"> + <option value="BrBg">BrBg: Brown - Blue Green</option> + <option value="PiYg">PiYg: Pink - Yellow Green</option> + <option value="PRGn">PRGn: Purple Red - Green</option> + <option value="PuOr">PuOr: Purple - Orange</option> + <option value="RdBu" selected="true">RdBu: Red - Blue</option> + <option value="RdGy">RdGy: Red - Gray</option> + <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> + <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> + <option value="Spectral">Spectral</option> + </param> + </xml> + + <xml name="general_options"> + <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> + <conditional name="ucol"> + <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" + help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically"> + <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option> + <option value="collect">Convert a collection of suitable track files</option> + </param> + <when value="collect"> + <param label="Collection of bed, bam and other track files" name="autoCollection" type="data_collection" /> + </when> + <when value="form"> + </when> + </conditional> + + <param label="Create a zip archive for downloading rather than viewing " name="zipOut" help="Default is to make an interactive browser appear when the 'eye' icon is activated" + type="boolean" checked="false" truevalue="true" falsevalue="false" /> + <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/> + <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/> + <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" /> + + <param name="primary_color" type="color" label="Primary color" value="#0D233F"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + <param name="secondary_color" type="color" label="Secondary color" value="#721E63"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + <param name="tertiary_color" type="color" label="Tertiary color" value="#135560"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + + <param label="Font size" name="font_size" type="integer" value="10" /> + </section> + </xml> + + <xml name="color_selection_minmax"> + <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> + <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the + auto case as well, but may be safe to just say "brewer colors? Pff, + red/blue" --> + <expand macro="auto_manual_tk" + token_cond_label="Color" + token_cond_name="color" + token_select_label="Color Selection" + token_select_name="color_select" + token_automatic_label="Automatically selected" + token_manual_label="Manual Color Selection"> + <expand macro="jb_color" + label="JBrowse style.pos_color" + name="style_pos_color" + value="blue" + help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." /> + <expand macro="jb_color" + label="JBrowse style.neg_color" + name="style_neg_color" + value="red" + help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." /> + </expand> + + <conditional name="bicolor_pivot" label="Bicolor Pivot"> + <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select"> + <option value="zero" selected="true">Zero</option> + <option value="mean">Mean</option> + <option value="custom">Custom Value</option> + </param> + <when value="zero" /> + <when value="mean" /> + <when value="custom"> + <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." /> + </when> + </conditional> + </section> + </xml> + + <xml name="color_selection" + token_scaling_lin_select="true" + token_scaling_log_select="false" + > + <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> + <conditional name="color_score" label="JBrowse style.color & Score relationship"> + <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track"> + <option value="score">Based on score</option> + <option value="none" selected="true">Ignore score</option> + </param> + <when value="none"> + <!-- When no scaling is done, no scores available, then just let the + user choose a base color for the track --> + <expand macro="auto_color" /> + </when> + <when value="score"> + <!-- Scaling --> + <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" + help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution."> + <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> + <option value="logarithmic" selected="false">Logarithmic scaling</option> + <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> + </param> + + <!-- Scaling Bounds --> + <conditional name="score_scales" label="Minimum/Maximum values for track scores"> + <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select"> + <option value="automatic" selected="true">Automatically determined</option> + <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> + </param> + <when value="automatic" /> + <when value="manual"> + <param label="Minimum expected score" name="minimum" type="integer" value="0" /> + <param label="Maximum expected score" name="maximum" type="integer" value="100" /> + </when> + </conditional> + + <!-- Scale color --> + <conditional name="color_scheme" label="Color Scheme for scored features"> + <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme"> + <option value="opacity">Opacity (high scores = 1.0 opacity)</option> + <!--<option value="brewer">Brewer Color Schemes</option>--> + </param> + <when value="opacity"> + <!-- Single color selection mode --> + <expand macro="auto_color" /> + </when> + <!--<when value="brewer">--> + <!--[> Brewer continuum selection <]--> + <!--<expand macro="brewer_scheme" />--> + <!--</when>--> + </conditional> + </when> + </conditional> + </section> + </xml> + + <xml name="track_visibility"> + <param type="select" label="Track Visibility" name="track_visibility"> + <option value="default_off">Off when browser opens</option> + <option value="default_on" selected="true">On when browser opens</option> + </param> + </xml> + + <xml name="track_styling_linear"> + <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" /> + <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" /> + <param name="display_mode" type="select" label="Display mode"> + <option value="normal" selected="true">normal</option> + <option value="compact">compact</option> + <option value="reducedRepresentation">reducedRepresentation</option> + <option value="collapse">collapse</option> + </param> + <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/> + </xml> + + <xml name="track_styling_feature"> + <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> + <conditional name="track_style"> + <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> + <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> + <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> + <option value="LinearArcDisplay">LinearArcDisplay</option> + </param> + <when value="LinearPileupDisplay"> + <expand macro="track_styling_linear"/> + </when> + <when value="LinearBasicDisplay"> + <expand macro="track_styling_linear"/> + + <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729 + and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 --> + <param label="Features label" + type="text" + name="label" + value="jexl:get(feature,'name') || get(feature,'id')" + help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> + <sanitizer> + <valid initial="default"> + <add value="|" /> + <add value="{"/> + <add value="}"/> + <add value="!"/> + <add value="?"/> + <add value="+"/> + <add value="="/> + <add value="'"/> + </valid> + </sanitizer> + </param> + <param label="Features description" + type="text" + name="description" + value="jexl:get(feature,'note') || get(feature,'description')" + help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> + <sanitizer> + <valid initial="default"> + <add value="|" /> + <add value="{"/> + <add value="}"/> + <add value="!"/> + <add value="?"/> + <add value="+"/> + <add value="="/> + <add value="'"/> + </valid> + </sanitizer> + </param> + </when> + <when value="LinearArcDisplay"/> + </conditional> + </section> + </xml> + + <xml name="track_styling_xam"> + <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> + <conditional name="track_style"> + <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> + <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option> + <option value="LinearPileupDisplay">LinearPileupDisplay</option> + <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option> + </param> + <when value="LinearAlignmentsDisplay"/> + <when value="LinearPileupDisplay"/> + <when value="LinearSNPCoverageDisplay"> + <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> + <param name="minScore" label="Min score" type="integer" value="" optional="true"/> + <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> + </when> + </conditional> + </section> + </xml> + + <xml name="track_styling_vcf"> + <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> + <conditional name="track_style"> + <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> + <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option> + </param> + <when value="LinearVariantDisplay"> + <expand macro="track_styling_linear"/> + </when> + </conditional> + </section> + </xml> + + <xml name="track_styling_bigwig"> + <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> + <conditional name="track_style"> + <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> + <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option> + </param> + <when value="LinearWiggleDisplay"> + <param name="autoscale" type="select" label="Autoscale type"> + <option value="local" selected="true">Local</option> + <option value="global">Global</option> + <option value="globalsd">Global ± 3σ</option> + <option value="localsd">Local ± 3σ</option> + </param> + <param name="resolution" label="Resolution" type="integer" value="1"/> + <param name="summaryScoreMode" type="select" label="Autoscale type"> + <option value="max">Max</option> + <option value="min">Min</option> + <option value="avg">Avg</option> + <option value="whiskers" selected="true">Whiskers (combines all three)</option> + </param> + <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" /> + <param name="scaleType" type="select" label="Autoscale type"> + <option value="linear" selected="true">Linear</option> + <option value="log">Log</option> + </param> + <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> + <param name="minScore" label="Min score" type="integer" value="" optional="true"/> + <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> + </when> + </conditional> + </section> + </xml> + + <xml name="track_menu"> + <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> + <repeat name="track_menu" title="Track Menu"> + <param label="Menu action" + type="select" + name="menu_action" + help="Action performed when user clicks on the menu"> + <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option> + <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option> + <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option> + </param> + <param label="Menu label" + type="text" + name="menu_label" + help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> + <expand macro="menu_sanitize" /> + </param> + <param label="Menu title" + type="text" + name="menu_title" + help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> + <expand macro="menu_sanitize" /> + </param> + <param label="Menu url" + type="text" + name="menu_url" + help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> + <expand macro="menu_sanitize" /> + </param> + <param label="Menu icon" + type="select" + name="menu_icon" + help="Icon to display next to menu label"> + <option value="dijitIconBookmark" selected="true">Bookmark</option> + <option value="dijitIconSave">Save</option> + <option value="dijitIconPrint">Print</option> + <option value="dijitIconCut">Cut</option> + <option value="dijitIconCopy">Copy</option> + <option value="dijitIconClear">Clear</option> + <option value="dijitIconDelete">Delete</option> + <option value="dijitIconUndo">Undo</option> + <option value="dijitIconEdit">Edit</option> + <option value="dijitIconNewTask">New Task</option> + <option value="dijitIconEditTask">Edit Task</option> + <option value="dijitIconEditProperty">Edit Property</option> + <option value="dijitIconTask">Task</option> + <option value="dijitIconFilter">Filter</option> + <option value="dijitIconConfigure">Configure</option> + <option value="dijitIconSearch">Search</option> + <option value="dijitIconApplication">Application</option> + <option value="dijitIconChart">Chart</option> + <option value="dijitIconConnector">Connector</option> + <option value="dijitIconDatabase">Database</option> + <option value="dijitIconDocuments">Documents</option> + <option value="dijitIconMail">Mail</option> + <option value="dijitLeaf">Leaf</option> + <option value="dijitIconFile">File</option> + <option value="dijitIconFunction">Function</option> + <option value="dijitIconKey">Key</option> + <option value="dijitIconPackage">Package</option> + <option value="dijitIconSample">Sample</option> + <option value="dijitIconTable">Table</option> + <option value="dijitIconUsers">Users</option> + <option value="dijitIconFolderClosed">Folder Closed</option> + <option value="dijitIconFolderOpen">Folder Open</option> + <option value="dijitIconError">Error</option> + </param> + </repeat> + </section> + </xml> + + <xml name="menu_sanitize"> + <sanitizer> + <valid> + <add value="{"/> + <add value="}"/> + <add value="!"/> + <add value="?"/> + <add value="&"/> + <add value="+"/> + <add value="="/> + <add value="'"/> + <add value='"'/> + </valid> + </sanitizer> + </xml> + + <xml name="input_conditional" token_label="Track Data" token_format="data"> + <conditional name="useuri"> + <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> + </param> + <when value="history"> + <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> + </when> + <when value="uri"> + <param label="@LABEL@" name="annouri" 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> + </when> + </conditional> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s13059-016-0924-1</citation> + <citation type="doi">10.1101/gr.094607.109</citation> + </citations> + </xml> +</macros>
--- a/test-data/gff3/merlin.gff3 Tue Mar 19 02:33:40 2024 +0000 +++ b/test-data/gff3/merlin.gff3 Thu Mar 21 08:01:42 2024 +0000 @@ -1,38 +1,28 @@ -##gff-version 3 -##sequence-region Merlin 1 172788 -Merlin GeneMark.hmm gene 10 30 . + . ID=Merlin_1;seqid=Merlin -Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_1_mRNA;Parent=Merlin_1 -Merlin GeneMark.hmm CDS 14 20 1000 + 0 ID=Merlin_1_CDS ;Parent=Merlin_1_mRNA -Merlin GeneMark.hmm CDS 24 30 500 + 0 ID=Merlin_1_CDS ;Parent=Merlin_1_mRNA -Merlin GeneMark.hmm gene 14 30 . + . ID=Merlin_2;seqid=Merlin;color=#00ff00 -Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_2_mRNA;seqid=Merlin;color=#00ff00;Parent=Merlin_2 -Merlin GeneMark.hmm CDS 14 20 500 + 0 ID=Merlin_2_CDS ;Parent=Merlin_2_mRNA;color=#0000ff -Merlin GeneMark.hmm CDS 24 30 750 + 0 ID=Merlin_2_CDS ;Parent=Merlin_2_mRNA;color=#00ff00 -Merlin GeneMark.hmm gene 10 30 . + . ID=Merlin_3;seqid=Merlin -Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_3A_mRNA;Parent=Merlin_3;color=#0000ff -Merlin GeneMark.hmm CDS 14 18 1000 + 0 ID=Merlin_3A_CDS ;Parent=Merlin_3A_mRNA;color=#0000ff -Merlin GeneMark.hmm CDS 20 30 800 + 0 ID=Merlin_3A_CDS ;Parent=Merlin_3A_mRNA;color=#0000ff -Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_3B_mRNA;Parent=Merlin_3;color=#0000ff -Merlin GeneMark.hmm CDS 14 22 400 + 0 ID=Merlin_3B_CDS ;Parent=Merlin_3B_mRNA;color=#0000ff -Merlin GeneMark.hmm CDS 24 30 1000 + 0 ID=Merlin_3B_CDS ;Parent=Merlin_3B_mRNA;color=#0000ff -Merlin exonerate gene 1740 2300 . + . Name=Apple3;Note=Gene with two splicing models;ID=1 -Merlin exonerate mRNA 1740 2300 . + . Name=Apple3-a;Note=mRNA A with both CDSs and UTRs;ID=1A;Parent=1; -Merlin exonerate UTR 1740 1799 . + . Parent=1A -Merlin exonerate CDS 1900 2080 . + 0 Parent=1A -Merlin exonerate CDS 2100 2120 . + 2 Parent=1A -Merlin exonerate UTR 2120 2300 . + . Parent=1A -Merlin exonerate mRNA 1740 2300 . + . Name=Apple3-b;Note=mRNA B with both CDSs and UTRs;ID=1B;Parent=1; -Merlin exonerate UTR 1740 1799 . + . Parent=1B -Merlin exonerate CDS 1800 1880 . + 0 Parent=1B -Merlin exonerate CDS 1900 1950 . + 1 Parent=1B -Merlin exonerate CDS 2100 2120 . + 2 Parent=1B -Merlin exonerate UTR 2120 2300 . + . Parent=1B -# { -# "baseUrl": "http://localhost:8000/out/data/" -# "compress": 0, -# "label": "Transcript", -# "storeClass": "JBrowse/Store/SeqFeature/NCList", -# "trackType": "JBrowse/View/Track/CanvasFeatures", -# "type": "JBrowse/View/Track/CanvasFeatures", -# "urlTemplate": "tracks/42ff9cb16c0509f0abb4a76ce14077bc_0/{refseq}/trackData.json", -# } +##gff-version3 +##sequence-region Merlin 1 172788 +Merlin GeneMark.hmm gene 10 30 . + . ID=Merlin_1;seqid=Merlin +Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_1_mRNA;Parent=Merlin_1 +Merlin GeneMark.hmm CDS14 20 1000 + 0 ID=Merlin_1_CDS;Parent=Merlin_1_mRNA +Merlin GeneMark.hmm CDS24 30 500+ 0 ID=Merlin_1_CDS;Parent=Merlin_1_mRNA +Merlin GeneMark.hmm gene 14 30 . + . ID=Merlin_2;seqid=Merlin;color=#00ff00 +Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_2_mRNA;seqid=Merlin;color=#00ff00;Parent=Merlin_2 +Merlin GeneMark.hmm CDS14 20 500+ 0 ID=Merlin_2_CDS;Parent=Merlin_2_mRNA;color=#0000ff +Merlin GeneMark.hmm CDS24 30 750+ 0 ID=Merlin_2_CDS;Parent=Merlin_2_mRNA;color=#00ff00 +Merlin GeneMark.hmm gene 10 30 . + . ID=Merlin_3;seqid=Merlin +Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_3A_mRNA;Parent=Merlin_3;color=#0000ff +Merlin GeneMark.hmm CDS14 18 1000 + 0 ID=Merlin_3A_CDS;Parent=Merlin_3A_mRNA;color=#0000ff +Merlin GeneMark.hmm CDS20 30 800+ 0 ID=Merlin_3A_CDS;Parent=Merlin_3A_mRNA;color=#0000ff +Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_3B_mRNA;Parent=Merlin_3;color=#0000ff +Merlin GeneMark.hmm CDS14 22 400+ 0 ID=Merlin_3B_CDS;Parent=Merlin_3B_mRNA;color=#0000ff +Merlin GeneMark.hmm CDS24 30 1000 + 0 ID=Merlin_3B_CDS;Parent=Merlin_3B_mRNA;color=#0000ff +Merlin exonerate gene 1740 2300 . + . Name=Apple3;Note=Genewithtwosplicingmodels;ID=1 +Merlin exonerate mRNA 1740 2300 . + . Name=Apple3-a;Note=mRNAAwithbothCDSsandUTRs;ID=1A;Parent=1; +# { +# "baseUrl":"http://localhost:8000/out/data/" +# "compress":0, +# "label":"Transcript", +# "storeClass":"JBrowse/Store/SeqFeature/NCList", +# "trackType":"JBrowse/View/Track/CanvasFeatures", +# "type":"JBrowse/View/Track/CanvasFeatures", +# "urlTemplate":"tracks/42ff9cb16c0509f0abb4a76ce14077bc_0/{refseq}/trackData.json", +# }