| Previous changeset 56:c0097a584a8a (2024-03-19) Next changeset 58:0e592dcaeb7f (2024-03-21) |
|
Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty |
|
modified:
autogenJB2.py convertMAF.sh jb2_urlconf.py jbrowse2.py jbrowse2.xml test-data/gff3/merlin.gff3 |
|
added:
jbrowse2broken.py jbrowse2broken.xml macrosbroken.xml |
| b |
| diff -r c0097a584a8a -r 94264fe60478 autogenJB2.py --- 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 |
| b |
| diff -r c0097a584a8a -r 94264fe60478 convertMAF.sh --- a/convertMAF.sh Tue Mar 19 02:33:40 2024 +0000 +++ b/convertMAF.sh Thu Mar 21 08:01:42 2024 +0000 |
| b |
| @@ -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 |
| b |
| diff -r c0097a584a8a -r 94264fe60478 jb2_urlconf.py --- 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)) |
| b |
| diff -r c0097a584a8a -r 94264fe60478 jbrowse2.py --- a/jbrowse2.py Tue Mar 19 02:33:40 2024 +0000 +++ b/jbrowse2.py Thu Mar 21 08:01:42 2024 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-#!/usr/bin/env python\n+ #!/usr/bin/env python\n # change to accumulating all configuration for config.json based on the default from the clone\n import argparse\n import binascii\n@@ -10,7 +10,6 @@\n import shutil\n import struct\n import subprocess\n-import sys\n import tempfile\n import urllib.request\n import xml.etree.ElementTree as ET\n@@ -480,9 +479,11 @@\n else:\n self.genome_firstcontig = fl\n else:\n- fl = urllib.request.urlopen(fapath+".fai").readline()\n- if fl: # is first row of the text fai so the first contig name\n- self.genome_firstcontig = fl.decode(\'utf8\').strip().split()[0]\n+ fl = urllib.request.urlopen(fapath + ".fai").readline()\n+ if fl: # is first row of the text fai so the first contig name\n+ self.genome_firstcontig = (\n+ fl.decode("utf8").strip().split()[0]\n+ )\n if self.config_json.get("assemblies", None):\n self.config_json["assemblies"] += assemblies\n else:\n@@ -538,6 +539,16 @@\n "adapter": adapter,\n },\n "rendering": {"type": "DivSequenceRenderer"},\n+ "displays": [\n+ {\n+ "type": "LinearReferenceSequenceDisplay",\n+ "displayId": "%s-LinearReferenceSequenceDisplay" % gname,\n+ },\n+ {\n+ "type": "LinearGCContentDisplay",\n+ "displayId": "%s-LinearGCContentDisplay" % gname,\n+ },\n+ ],\n }\n return trackDict\n \n@@ -604,13 +615,15 @@\n uri = data\n else:\n uri = trackData["hic_url"]\n- categ = trackData[\'category\']\n+ categ = trackData["category"]\n trackDict = {\n "type": "HicTrack",\n "trackId": tId,\n "name": uri,\n "assemblyNames": [self.genome_name],\n- "category": [categ,],\n+ "category": [\n+ categ,\n+ ],\n "adapter": {\n "type": "HicAdapter",\n "hicLocation": uri,\n@@ -622,8 +635,6 @@\n },\n ],\n }\n- style_json = self._prepare_track_style(trackDict)\n- trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -643,7 +654,7 @@\n }\n ]\n }\n- categ = trackData[\'category\']\n+ categ = trackData["category"]\n fname = "%s.bed" % tId\n dest = "%s/%s" % (self.outdir, fname)\n gname = self.genome_name\n@@ -665,11 +676,14 @@\n soutp = outp.split("\\n")\n samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")]\n samples = [x.split(".")[0] for x in samp]\n+ logging.warn("### maf convert cmd = %s,\\nsamples=%s" % (\' \'.join(cmd), samples))\n trackDict = {\n "type": "MafTrack",\n "trackId": tId,\n "name": trackData["name"],\n- "category": [categ,],\n+ "category": [\n+ categ,\n+ ],\n "adapter": {\n "type": "MafTabixAdapter",\n "samples": samples,\n@@ -694,8 +708,6 @@\n },\n ],\n }\n- style_json = self._prepare_track_style(trackDict)\n- trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n if self.config_json.get("plugins", None):\n@@ -717,11 +729,11 @@\n ]\n subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)\n gff3_unrebased.close()\n+ logging.warn("### blastxml to gff3 cmd = %s" % \' \'.join(cmd))\n return gff3_unrebased.name\n \n def add_blastxml(self,'..b'_name,\n- "start": 2000,\n- "end": 200000,\n+ "start": 1,\n+ "end": 100000,\n "refName": "x",\n }\n \n- if data.get("defaultLocation", ""):\n- ddl = data["defaultLocation"]\n+ if default_data.get("defaultLocation", ""):\n+ ddl = default_data["defaultLocation"]\n loc_match = re.search(r"^([^:]+):([\\d,]*)\\.*([\\d,]*)$", ddl)\n # allow commas like 100,000 but ignore as integer\n if loc_match:\n@@ -1324,7 +1338,7 @@\n logging.info(\n "@@@ no contig name found for default session - please add one!"\n )\n- session_name = data.get("session_name", "New session")\n+ session_name = default_data.get("session_name", "New session")\n for key, value in mapped_chars.items():\n session_name = session_name.replace(value, key)\n # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)\n@@ -1382,7 +1396,9 @@\n """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now"""\n dest = self.outdir\n if realclone:\n- self.subprocess_check_call([\'jbrowse\', \'create\', dest,"-f", \'--tag\', f"{JB2VER}"])\n+ self.subprocess_check_call(\n+ ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]\n+ )\n else:\n shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)\n for fn in [\n@@ -1400,14 +1416,8 @@\n \n \n def parse_style_conf(item):\n- if "type" in item.attrib and item.attrib["type"] in [\n- "boolean",\n- "integer",\n- ]:\n- if item.attrib["type"] == "boolean":\n- return item.text in ("yes", "true", "True")\n- elif item.attrib["type"] == "integer":\n- return int(item.text)\n+ if item.text.lower() in [\'false\',\'true\',\'yes\',\'no\']:\n+ return item.text.lower in ("yes", "true")\n else:\n return item.text\n \n@@ -1473,6 +1483,7 @@\n trackfiles = track.findall("files/trackFile")\n if trackfiles:\n for x in track.findall("files/trackFile"):\n+ track_conf["label"] = x.attrib["label"]\n track_conf["useuri"] = x.attrib["useuri"]\n if is_multi_bigwig:\n multi_bigwig_paths.append(\n@@ -1521,6 +1532,11 @@\n track_conf["style"] = {\n item.tag: parse_style_conf(item) for item in track.find("options/style")\n }\n+ else:\n+ track_conf["style"] = {}\n+ tst = track_conf["style"].get("type", None)\n+ if tst:\n+ track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst)\n if track.find("options/style_labels"):\n track_conf["style_labels"] = {\n item.tag: parse_style_conf(item)\n@@ -1530,12 +1546,6 @@\n track_conf["conf"] = etree_to_dict(track.find("options"))\n track_conf["category"] = track.attrib["cat"]\n track_conf["format"] = track.attrib["format"]\n- try:\n- # Only pertains to gff3 + blastxml. TODO?\n- track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}\n- except TypeError:\n- track_conf["style"] = {}\n- pass\n keys = jc.process_annotations(track_conf)\n \n if keys:\n@@ -1544,9 +1554,7 @@\n track.attrib.get("visibility", "default_off")\n ].append(key)\n if track_conf.get("style", None):\n- default_session_data["style"][key] = track_conf[\n- "style"\n- ] # TODO do we need this anymore?\n+ default_session_data["style"][key] = track_conf["style"]\n if track_conf.get("style_lables", None):\n default_session_data["style_labels"][key] = track_conf.get(\n "style_labels", None\n' |
| b |
| diff -r c0097a584a8a -r 94264fe60478 jbrowse2.xml --- 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"> |
| b |
| diff -r c0097a584a8a -r 94264fe60478 jbrowse2broken.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse2broken.py Thu Mar 21 08:01:42 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1656 @@\n+#!/usr/bin/env python\n+# change to accumulating all configuration for config.json based on the default from the clone\n+import argparse\n+import binascii\n+import datetime\n+import json\n+import logging\n+import os\n+import re\n+import shutil\n+import struct\n+import subprocess\n+import tempfile\n+import urllib.request\n+import xml.etree.ElementTree as ET\n+from collections import defaultdict\n+\n+logging.basicConfig(level=logging.INFO)\n+log = logging.getLogger("jbrowse")\n+\n+JB2VER = "v2.10.3"\n+# version pinned for cloning\n+\n+TODAY = datetime.datetime.now().strftime("%Y-%m-%d")\n+GALAXY_INFRASTRUCTURE_URL = None\n+\n+# version pinned for cloning\n+\n+mapped_chars = {\n+ ">": "__gt__",\n+ "<": "__lt__",\n+ "\'": "__sq__",\n+ \'"\': "__dq__",\n+ "[": "__ob__",\n+ "]": "__cb__",\n+ "{": "__oc__",\n+ "}": "__cc__",\n+ "@": "__at__",\n+ "#": "__pd__",\n+ "": "__cn__",\n+}\n+\n+\n+class ColorScaling(object):\n+\n+ COLOR_FUNCTION_TEMPLATE = """\n+ function(feature, variableName, glyphObject, track) {{\n+ var score = {score};\n+ {opacity}\n+ return \'rgba({red}, {green}, {blue}, \' + opacity + \')\';\n+ }}\n+ """\n+\n+ COLOR_FUNCTION_TEMPLATE_QUAL = r"""\n+ function(feature, variableName, glyphObject, track) {{\n+ var search_up = function self(sf, attr){{\n+ if(sf.get(attr) !== undefined){{\n+ return sf.get(attr);\n+ }}\n+ if(sf.parent() === undefined) {{\n+ return;\n+ }}else{{\n+ return self(sf.parent(), attr);\n+ }}\n+ }};\n+\n+ var search_down = function self(sf, attr){{\n+ if(sf.get(attr) !== undefined){{\n+ return sf.get(attr);\n+ }}\n+ if(sf.children() === undefined) {{\n+ return;\n+ }}else{{\n+ var kids = sf.children();\n+ for(var child_idx in kids){{\n+ var x = self(kids[child_idx], attr);\n+ if(x !== undefined){{\n+ return x;\n+ }}\n+ }}\n+ return;\n+ }}\n+ }};\n+\n+ var color = ({user_spec_color} || search_up(feature, \'color\') || search_down(feature, \'color\') || {auto_gen_color});\n+ var score = (search_up(feature, \'score\') || search_down(feature, \'score\'));\n+ {opacity}\n+ if(score === undefined){{ opacity = 1; }}\n+ var result = /^#?([a-f\\d]{{2}})([a-f\\d]{{2}})([a-f\\d]{{2}})$/i.exec(color);\n+ var red = parseInt(result[1], 16);\n+ var green = parseInt(result[2], 16);\n+ var blue = parseInt(result[3], 16);\n+ if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}\n+ return \'rgba(\' + red + \',\' + green + \',\' + blue + \',\' + opacity + \')\';\n+ }}\n+ """\n+\n+ OPACITY_MATH = {\n+ "linear": """\n+ var opacity = (score - ({min})) / (({max}) - ({min}));\n+ """,\n+ "logarithmic": """\n+ var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));\n+ """,\n+ "blast": """\n+ var opacity = 0;\n+ if(score == 0.0) {{\n+ opacity = 1;\n+ }} else {{\n+ opacity = (20 - Math.log10(score)) / 180;\n+ }}\n+ """,\n+ }\n+\n+ BREWER_COLOUR_IDX = 0\n+ BREWER_COLOUR_SCHEMES = [\n+ (166, 206, 227),\n+ (31, 120, 180),\n+ (178, 223, 138),\n+ (51, 160, 44),\n+ (251, 154, 153),\n+ (227, 26, 28),\n+ (253, 191, 111),\n+ (255, 127, 0),\n+ (202, 178, 214),\n+ (106, 61, 154),\n+ (255, 255, 153),\n+ (177, 89, 40),\n+ (228, 26, 28),\n+ (55, 126, 184),\n+ (77, 175, 74),\n+ (152, 78, 163),\n+ (255, 127, 0),\n+ ]\n+\n+ BREWER_DIVERGING_PALLETES = {\n+ "BrBg": ("#543005", "#003c30"),\n+ "PiYg": ("#8e0152", "#276419"),\n+ "PRGn": ("#40004b", "#00441b"),\n+ "PuOr": ("#7f3b08", "#2d004b'..b'"],\n+ x.attrib["useuri"],\n+ x.attrib["label"],\n+ metadata,\n+ )\n+ else:\n+ tfa = (\n+ os.path.realpath(x.attrib["path"]),\n+ x.attrib["ext"],\n+ x.attrib["useuri"],\n+ x.attrib["label"],\n+ metadata,\n+ )\n+ track_conf["trackfiles"].append(tfa)\n+\n+ if is_multi_bigwig:\n+ metadata = metadata_from_node(x.find("metadata"))\n+\n+ track_conf["trackfiles"].append(\n+ (\n+ multi_bigwig_paths, # Passing an array of paths to represent as one track\n+ "bigwig_multiple",\n+ "MultiBigWig", # Giving an hardcoded name for now\n+ {}, # No metadata for multiple bigwig\n+ )\n+ )\n+ track_conf["category"] = track.attrib["cat"]\n+ track_conf["format"] = track.attrib["format"]\n+ if track.find("options/style"):\n+ track_conf["style"] = {\n+ item.tag: parse_style_conf(item) for item in track.find("options/style")\n+ }\n+ else:\n+ track_conf["style"] = {}\n+ tst = track_conf["style"].get("type", None)\n+ if tst:\n+ track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst)\n+ logging.warn("### got %s for track style" % track_conf["style"])\n+ if track.find("options/style_labels"):\n+ track_conf["style_labels"] = {\n+ item.tag: parse_style_conf(item)\n+ for item in track.find("options/style_labels")\n+ }\n+ track_conf["conf"] = etree_to_dict(track.find("options"))\n+ track_conf["category"] = track.attrib["cat"]\n+ track_conf["format"] = track.attrib["format"]\n+ keys = jc.process_annotations(track_conf)\n+\n+ if keys:\n+ for key in keys:\n+ default_session_data["visibility"][\n+ track.attrib.get("visibility", "default_off")\n+ ].append(key)\n+ if track_conf.get("style", None):\n+ default_session_data["style"][key] = track_conf["style"]\n+ if track_conf.get("style_labels", None):\n+ default_session_data["style_labels"][key] = track_conf.get(\n+ "style_labels", None\n+ )\n+ logging.warn(\n+ "# after process, key=%s def session style = %s"\n+ % (key, default_session_data["style"][key])\n+ )\n+ default_session_data["defaultLocation"] = root.find(\n+ "metadata/general/defaultLocation"\n+ ).text\n+ default_session_data["session_name"] = root.find(\n+ "metadata/general/session_name"\n+ ).text\n+ jc.zipOut = root.find("metadata/general/zipOut").text == "true"\n+ general_data = {\n+ "analytics": root.find("metadata/general/analytics").text,\n+ "primary_color": root.find("metadata/general/primary_color").text,\n+ "secondary_color": root.find("metadata/general/secondary_color").text,\n+ "tertiary_color": root.find("metadata/general/tertiary_color").text,\n+ "quaternary_color": root.find("metadata/general/quaternary_color").text,\n+ "font_size": root.find("metadata/general/font_size").text,\n+ }\n+ jc.add_general_configuration(general_data)\n+ trackconf = jc.config_json.get("tracks", None)\n+ if trackconf:\n+ jc.config_json["tracks"].update(jc.tracksToAdd)\n+ else:\n+ jc.config_json["tracks"] = jc.tracksToAdd\n+ jc.write_config()\n+ jc.add_default_session(default_session_data)\n+ logging.warn("### got default_session_data=%s" % default_session_data)\n+ # jc.text_index() not sure what broke here.\n' |
| b |
| diff -r c0097a584a8a -r 94264fe60478 jbrowse2broken.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse2broken.xml Thu Mar 21 08:01:42 2024 +0000 |
| [ |
| b'@@ -0,0 +1,961 @@\n+ <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_7" profile="22.05">\n+ <description>genome browser</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edamInc"/>\n+ <xrefs>\n+ <xref type="bio.tools">jbrowse2</xref>\n+ </xrefs>\n+ <expand macro="requirements"/>\n+ <version_command>python \'${__tool_directory__}/jbrowse2.py\' --version</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+mkdir -p \'$output.files_path\' &&\n+## Copy the XML file into the directory, mostly for debugging\n+## but nice if users want to reproduce locally\n+cp \'$trackxml\' \'$output.files_path/galaxy.xml\' &&\n+\n+export JBROWSE2_PATH=\\$(dirname \\$(which jbrowse))/../opt/jbrowse2 &&\n+\n+#if $jbgen.ucol.formcoll=="collect":\n+ python \'$__tool_directory__/autogenJB2.py\'\n+ #for $key in $autoCollection.keys():\n+ #if $autoCollection[$key].is_collection:\n+ #set subCol=$autoCollection[$key]\n+ #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == \'paf\']\n+ #if len($pafs) > 0:\n+ --pafmeta \'$pafs[0]\'\n+ #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == \'fasta\']\n+ #for $ref in $refs:\n+ --pafreferencemeta \'$ref\'\n+ #end for\n+ #end if\n+ #else if $autoCollection[$key].ext == \'fasta\':\n+ --referencemeta \'$autoCollection[$key],$autoCollection[$key].ext,$key\'\n+ #else if $autoCollection[$key].ext in [\'bed\', \'bigwig\', \'cool\', \'gff\', \'gff3\', \'hic\', \'maf\', \'mcool\', \'scool\', \'vcf\']\n+ --trackmeta \'$autoCollection[$key],$autoCollection[$key].ext,$key\'\n+ #else if $autoCollection[$key].ext in [\'bam\',]\n+ --trackmeta \'$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index\'\n+ #else if $autoCollection[$key].ext in [\'cram\',]\n+ --trackmeta \'$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index\'\n+ #end if\n+ #end for\n+ --outdir \'$output.files_path\'\n+ --jbrowse2path \\${JBROWSE2_PATH}\n+ --sessName "Autogen JBrowse" &&\n+ #if $jbgen.zipOut == "true":\n+ (cd \'$output.files_path\' && zip -r - . ) > \'$output\'\n+ #else\n+ cp \'$output.files_path/index.html\' \'$output\'\n+ #end if\n+#else:\n+ python \'$__tool_directory__/jbrowse2.py\'\n+ --jbrowse2path \\${JBROWSE2_PATH}\n+ --outdir \'$output.files_path\'\n+ --xml \'$trackxml\' &&\n+ #if $jbgen.zipOut == "true":\n+ (cd \'$output.files_path\' && zip -r - . ) > \'$output\'\n+ #else\n+ cp \'$output.files_path/index.html\' \'$output\'\n+ #end if\n+ ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.\n+ #if str($uglyTestingHack) == "enabled":\n+ && cp \'$trackxml\' \'$output\'\n+ #end if\n+#end if\n+ ]]></command>\n+<configfiles>\n+ <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>\n+#if $jbgen.ucol.formcoll=="form":\n+<root>\n+ <metadata>\n+ <genomes>\n+ #if str($reference_genome.genome_type_select) == "uri":\n+ <genome path="${reference_genome.uri}" label="${reference_genome.refname}" useuri="yes">\n+ <metadata>\n+ <dataset\n+ dname = "${reference_genome.refname}" />\n+ </metadata>\n+ </genome>\n+ #else if str($reference_genome.genome_type_select) == "indexed":\n+ <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no">\n+ <metadata>\n+ <dataset\n+ dname = "${reference_genome.genome.fields.name}" />\n+ </metadata>\n+ </genome>\n+ #else\n+ <genome path="$reference_genome.genome" label="${reference_genome.gen'..b'ternative codons for unusual genomes,\n+and detailed track styling is not yet implemented. Send code.\n+JBrowse1 development has now ceased in favour of JBrowse2.\n+\n+Use and local viewing\n+=====================\n+\n+\n+A JBrowse2 history item can be opened by viewing it (the "eye" icon).\n+\n+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.\n+This can be shared and viewed without Galaxy.\n+\n+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,\n+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\n+directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*\n+\n+With python3 installed,\n+\n+*python3 jb2_webserver.py*\n+\n+will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,\n+but the script appears to be running, try pointing your web browser to the default of *localhost:8080*\n+\n+Overview\n+--------\n+\n+JBrowse is a fast, embeddable genome browser built completely with\n+JavaScript and HTML5.\n+\n+The JBrowse-in-Galaxy (JiG) tool was written to help build complex\n+JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying\n+about how to run the command line tools to format your data, and which\n+options need to be supplied and where.\n+\n+Options\n+-------\n+\n+**Reference or Assembly**\n+\n+Choose either a built-in or select one from your history.\n+\n+Track coordinates and contig names *must* match this reference precisely\n+or they will not display.\n+\n+**Track Groups** represent a set of tracks in a single category.\n+\n+Annotation Tracks\n+-----------------\n+\n+GFF3/BED\n+~~~~~~~~\n+\n+Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.\n+\n+When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads\n+to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is\n+selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works\n+well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the\n+lengths of each assembly or reference contig.\n+\n+BAM Pileups\n+~~~~~~~~~~~\n+\n+We support BAM files and can automatically generate SNP tracks based on\n+that bam data.\n+\n+\n+BlastXML\n+~~~~~~~~\n+\n+JiG now supports both blastn and blastp datasets. JiG internally uses a\n+blastXML to gapped GFF3 tool to convert your blastxml datasets into a\n+format amenable to visualization in JBrowse. This tool is also\n+available separately from the IUC on the toolshed.\n+\n+**Minimum Gap Size** reflects how long a gap must be before it becomes a\n+real gap in the processed gff3 file. In the picture above, various sizes\n+of gaps can be seen. If the minimum gap size was set much higher, say\n+100nt, many of the smaller gaps would disappear, and the features on\n+both sides would be merged into one, longer feature. This setting is\n+inversely proportional to runtime and output file size. *Do not set this\n+to a low value for large datasets*. By setting this number lower, you\n+will have extremely large outputs and extremely long runtimes. The\n+default was configured based off of the author\'s experience, but the\n+author only works on small viruses. It is *strongly* recommended that\n+you filter your blast results before display, e.g. picking out the top\n+10 hits or so.\n+\n+**Protein blast search** option merely informs underlying tools that\n+they should adjust feature locations by 3x.\n+\n+\n+@ATTRIBUTION@\n+]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
| b |
| diff -r c0097a584a8a -r 94264fe60478 macrosbroken.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macrosbroken.xml Thu Mar 21 08:01:42 2024 +0000 |
| [ |
| b'@@ -0,0 +1,548 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@TOOL_VERSION@">2.10.1</token>\n+ <xml name = "edamInc">\n+ <edam_topics>\n+ <edam_topic>topic_3307</edam_topic>\n+ <edam_topic>topic_0092</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_0573</edam_operation>\n+ <edam_operation>operation_0564</edam_operation>\n+ </edam_operations>\n+ </xml>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>\n+ <requirement type="package" version="1.81">biopython</requirement>\n+ <requirement type="package" version="0.7.1">bcbio-gff</requirement>\n+ <requirement type="package" version="1.19">samtools</requirement>\n+ <requirement type="package" version="6.0.1">pyyaml</requirement>\n+ <requirement type="package" version="1.11">tabix</requirement>\n+ <requirement type="package" version="4.6.0">findutils</requirement>\n+ <requirement type="package" version="0.0.8">hictk</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <token name="@DATA_DIR@">\\$GALAXY_JBROWSE_SHARED_DIR</token>\n+ <token name="@WRAPPER_VERSION@">galaxy2</token>\n+ <token name="@ATTRIBUTION@"><![CDATA[\n+**Attribution**\n+This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is maintained by Ross Lazarus\n+until the IUC complete their own.\n+]]>\n+ </token>\n+ <xml name="genome_selector"\n+ token_help=""\n+ token_label="Fasta sequences"\n+ token_optional="False" >\n+ <conditional name="reference_genome">\n+ <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">\n+ <option selected="True" value="indexed">Use a built-in genome</option>\n+ <option value="history">Use a genome from history</option>\n+ </param>\n+ <when value="indexed">\n+ <param\n+ help="@HELP@"\n+ label="@LABEL@"\n+ name="genomes"\n+ type="select"\n+ optional="@OPTIONAL@"\n+ >\n+ <options from_data_table="all_fasta">\n+ <filter column="2" type="sort_by" />\n+ <validator message="No genomes are available for the selected input dataset" type="no_options" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param\n+ format="fasta"\n+ label="@LABEL@"\n+ help="@HELP@"\n+ name="genomes"\n+ type="data"\n+ optional="@OPTIONAL@"\n+ multiple="True" />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="auto_manual_tk"\n+ token_cond_label="Color"\n+ token_cond_name="color"\n+ token_select_label="Color Specification"\n+ token_select_name="color_select"\n+ token_automatic_label="Automatically selected"\n+ token_manual_label="Manual Color Selection">\n+ <conditional name="@COND_NAME@" label="@COND_LABEL@">\n+ <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">\n+ <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>\n+ <option value="manual">@MANUAL_LABEL@</option>\n+ </param>\n+ <when value="automatic">\n+ </when>\n+ <when value="manual">\n+ <yield />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="jb_color"\n+ token_label="JBrowse style.color"\n+ token_name="style_color"\n+ token_value="goldenrod"\n+ token_help="Basic color of features. Most glyphs interpret this as the fill col'..b'>\n+ <option value="dijitIconUndo">Undo</option>\n+ <option value="dijitIconEdit">Edit</option>\n+ <option value="dijitIconNewTask">New Task</option>\n+ <option value="dijitIconEditTask">Edit Task</option>\n+ <option value="dijitIconEditProperty">Edit Property</option>\n+ <option value="dijitIconTask">Task</option>\n+ <option value="dijitIconFilter">Filter</option>\n+ <option value="dijitIconConfigure">Configure</option>\n+ <option value="dijitIconSearch">Search</option>\n+ <option value="dijitIconApplication">Application</option>\n+ <option value="dijitIconChart">Chart</option>\n+ <option value="dijitIconConnector">Connector</option>\n+ <option value="dijitIconDatabase">Database</option>\n+ <option value="dijitIconDocuments">Documents</option>\n+ <option value="dijitIconMail">Mail</option>\n+ <option value="dijitLeaf">Leaf</option>\n+ <option value="dijitIconFile">File</option>\n+ <option value="dijitIconFunction">Function</option>\n+ <option value="dijitIconKey">Key</option>\n+ <option value="dijitIconPackage">Package</option>\n+ <option value="dijitIconSample">Sample</option>\n+ <option value="dijitIconTable">Table</option>\n+ <option value="dijitIconUsers">Users</option>\n+ <option value="dijitIconFolderClosed">Folder Closed</option>\n+ <option value="dijitIconFolderOpen">Folder Open</option>\n+ <option value="dijitIconError">Error</option>\n+ </param>\n+ </repeat>\n+ </section>\n+ </xml>\n+\n+ <xml name="menu_sanitize">\n+ <sanitizer>\n+ <valid>\n+ <add value="{"/>\n+ <add value="}"/>\n+ <add value="!"/>\n+ <add value="?"/>\n+ <add value="&"/>\n+ <add value="+"/>\n+ <add value="="/>\n+ <add value="\'"/>\n+ <add value=\'"\'/>\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+\n+ <xml name="input_conditional" token_label="Track Data" token_format="data">\n+ <conditional name="useuri">\n+ <param name="insource" type="select" label="Define track data as a history file or an internet URI"\n+ help="A public URI implies that all the associated tabix files are also in place. They are created for history files">\n+ <option value="history" selected="true">Track data from a history file</option>\n+ <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option>\n+ </param>\n+ <when value="history">\n+ <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />\n+ </when>\n+ <when value="uri">\n+ <param label="@LABEL@" name="annouri" type="text" />\n+ <param label="Short name for track display" name="annoname" type="text" >\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable" >\n+ <remove value="\'" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1186/s13059-016-0924-1</citation>\n+ <citation type="doi">10.1101/gr.094607.109</citation>\n+ </citations>\n+ </xml>\n+</macros>\n' |
| b |
| diff -r c0097a584a8a -r 94264fe60478 test-data/gff3/merlin.gff3 --- 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 |
| b |
| @@ -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", +# } |