| Previous changeset 59:f807e219cec3 (2024-03-22) Next changeset 61:e7a6f7a7148d (2024-03-26) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a |
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modified:
autogenJB2.py jbrowse2.py jbrowse2.xml macros.xml |
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| diff -r f807e219cec3 -r 81d535970196 autogenJB2.py --- a/autogenJB2.py Fri Mar 22 22:04:08 2024 +0000 +++ b/autogenJB2.py Mon Mar 25 02:10:05 2024 +0000 |
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| @@ -172,8 +172,7 @@ for key in keys: if trext in [ "bigwig", - "gff3", - "gff", + "gff", "gff3", "vcf", "maf", ]: @@ -182,6 +181,16 @@ default_session_data["visibility"]["default_off"].append( key ) + if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]: + ttype = "LinearBasicDisplay" + if trext == "vcf": + ttype = "LinearVariantDisplay" + style_json = { + "type": ttype, + "trackShowLabels": False, + "trackShowDescriptions": False + } + default_session_data["style"][key] = style_json # general_data = { # "analytics": root.find("metadata/general/analytics").text, # "primary_color": root.find("metadata/general/primary_color").text, |
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| diff -r f807e219cec3 -r 81d535970196 jbrowse2.py --- a/jbrowse2.py Fri Mar 22 22:04:08 2024 +0000 +++ b/jbrowse2.py Mon Mar 25 02:10:05 2024 +0000 |
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| b'@@ -1,5 +1,5 @@\n #!/usr/bin/env python\n-# change to accumulating all configuration for config.json based on the default from the clone\n+\n import argparse\n import binascii\n import datetime\n@@ -24,8 +24,6 @@\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@@ -458,7 +456,7 @@\n genome_name = genome_name.split()[0]\n # spaces and cruft break scripts when substituted\n if genome_name not in self.genome_names:\n- # ignore dupes - can have multiple pafs with same references?\n+ # pafs with shared references\n fapath = genome_node["path"]\n if not useuri:\n fapath = os.path.realpath(fapath)\n@@ -467,7 +465,7 @@\n self.genome_names.append(genome_name)\n if self.genome_name is None:\n self.genome_name = (\n- genome_name # first one for all tracks - other than paf\n+ genome_name # first one for all tracks\n )\n self.genome_sequence_adapter = assem["sequence"]["adapter"]\n self.genome_firstcontig = None\n@@ -481,11 +479,16 @@\n else:\n self.genome_firstcontig = fl\n else:\n- fl = urllib.request.urlopen(fapath + ".fai").readline()\n+ try:\n+ fl = urllib.request.urlopen(fapath + ".fai").readline()\n+ except:\n+ fl = None\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+ else:\n+ self.genome_firstcontig = None\n if self.config_json.get("assemblies", None):\n self.config_json["assemblies"] += assemblies\n else:\n@@ -606,6 +609,8 @@\n gziLocation:\n uri: \'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi\',\n Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438\n+\n+\n """\n tId = trackData["label"]\n # can be served - if public.\n@@ -615,29 +620,25 @@\n if useuri:\n uri = data\n else:\n- uri = trackData["hic_url"]\n+ uri = "%s.hic" % trackData["label"]\n+ # slashes in names cause path trouble\n+ dest = os.path.join(self.outdir, uri)\n+ cmd = ["cp", data, dest]\n+ self.subprocess_check_call(cmd)\n categ = trackData["category"]\n trackDict = {\n "type": "HicTrack",\n "trackId": tId,\n- "name": uri,\n+ "name": trackData["name"],\n "assemblyNames": [self.genome_name],\n "category": [\n categ,\n ],\n "adapter": {\n "type": "HicAdapter",\n- "hicLocation": uri,\n- },\n- "displays": [\n- {\n- "type": "LinearHicDisplay",\n- "displayId": "%s-LinearHicDisplay" % tId,\n- },\n- ],\n+ "hicLocation": { "uri": uri }\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@@ -793,14 +794,6 @@\n os.unlink(gff3)\n \n def add_bigwig(self, data, trackData):\n- """ "type": "LinearWiggleDisplay",\n- "configuration": {},\n- "selectedRendering": "",\n- "resolution": 1,'..b'fault data for %s" % tId)\n+ logging.warn("### No style data in default data %s for %s" % (default_data, tId))\n style_data = {"type": "LinearBasicDisplay"}\n if "displays" in track_conf:\n disp = track_conf["displays"][0]["type"]\n@@ -1315,7 +1305,7 @@\n )\n # The view for the assembly we\'re adding\n view_json = {"type": "LinearGenomeView", "tracks": tracks_data}\n-\n+ logging.warn("### view_json=%s" % view_json)\n refName = None\n drdict = {\n "reversed": False,\n@@ -1408,8 +1398,10 @@\n with open(config_path, "w") as config_file:\n json.dump(self.config_json, config_file, indent=2)\n \n- def clone_jbrowse(self, realclone=True):\n- """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now"""\n+ def clone_jbrowse(self, realclone=False):\n+ """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now\n+ Leave as True between version updates on temporary tools - requires manual conda trigger :(\n+ """\n dest = self.outdir\n if realclone:\n self.subprocess_check_call(\n@@ -1472,7 +1464,6 @@\n )\n jc.process_genomes()\n \n- # .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py\n default_session_data = {\n "visibility": {\n "default_on": [],\n@@ -1500,6 +1491,7 @@\n if trackfiles:\n for x in track.findall("files/trackFile"):\n track_conf["label"] = x.attrib["label"]\n+ trackkey = track_conf["label"]\n track_conf["useuri"] = x.attrib["useuri"]\n if is_multi_bigwig:\n multi_bigwig_paths.append(\n@@ -1544,18 +1536,6 @@\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- 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-\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@@ -1566,12 +1546,20 @@\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_lables", None):\n- default_session_data["style_labels"][key] = track_conf.get(\n- "style_labels", None\n- )\n+ if track.find("options/style"):\n+ default_session_data["style"][key] = {\n+ item.tag: parse_style_conf(item) for item in track.find("options/style")\n+ }\n+ logging.warn("### added %s to defsess %s for %s" % (trackkey, default_session_data, key ))\n+ else:\n+ default_session_data["style"][key] = {}\n+ logging.warn("@@@@ no options/style found for %s" % (key))\n+\n+ if track.find("options/style_labels"):\n+ default_session_data["style_labels"][key] = {\n+ item.tag: parse_style_conf(item)\n+ for item in track.find("options/style_labels")\n+ }\n default_session_data["defaultLocation"] = root.find(\n "metadata/general/defaultLocation"\n ).text\n' |
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| diff -r f807e219cec3 -r 81d535970196 jbrowse2.xml --- a/jbrowse2.xml Fri Mar 22 22:04:08 2024 +0000 +++ b/jbrowse2.xml Mon Mar 25 02:10:05 2024 +0000 |
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| @@ -11,12 +11,8 @@ <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(): @@ -139,17 +135,15 @@ #for $tg in $track_groups: #for $track in $tg.data_tracks: #if $track.data_format.useuri.insource == "uri": - <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}"> + <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> <files> - <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf" - label="${track.data_format.useuri.insource.annoname}" useuri="yes"> + <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.insource.annouri}" /> + <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}"> @@ -157,7 +151,6 @@ #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="${dataset.datatype.edam_format}" @@ -193,23 +186,27 @@ </trackFile> #end for </files> - - <options> - <style> - #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "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 + #end if + <options> + <style> + #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]: + <type>${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>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> #end if - #if str($track.data_format.data_format_select) in ["bam", "cram"]: - <type>LinearAlignmentsDisplay</type> - #end if - #if str($track.data_format.data_format_select) in ["paf"]: - <type>LinearBasicDisplay</type> - #end if - </style> + #end if + #if str($track.data_format.data_format_select) in ["bam", "cram"]: + <type>LinearAlignmentsDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["paf"]: + <type>LinearBasicDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["hic"]: + <type>LinearHicDisplay</type> + #end if + </style> #if str($track.data_format.data_format_select) == "bam": <bam> #for $dataset in $track.data_format.useuri.annotation: @@ -268,8 +265,6 @@ #end if </options> </track> - #end if - #end if #end for #end for </tracks> |
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| diff -r f807e219cec3 -r 81d535970196 macros.xml --- a/macros.xml Fri Mar 22 22:04:08 2024 +0000 +++ b/macros.xml Mon Mar 25 02:10:05 2024 +0000 |
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| @@ -542,12 +542,12 @@ <xml name="pafref_conditional" token_label="Track Data" token_format="data"> <conditional name="pafuseuri"> <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" - help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> - <option value="history" selected="true">PAF genome reference data from a history file</option> - <option value="uri">PAF genome reference data from tabix data URI - index files must be available at corresponding URI</option> + help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> + <option value="history" selected="true">PAF reference comparison genome from a history file</option> + <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> </param> <when value="history"> - <repeat name="refgenomes" title="Add one or more comparison genomes used to make the PAF"> + <repeat name="refgenomes" title="PAF reference comparison genome used to make the PAF"> <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> <param label="Short name for track display" name="annoname" type="text" > <sanitizer invalid_char="_"> @@ -559,7 +559,7 @@ </repeat> </when> <when value="uri"> - <repeat name="refgenomes" title="Provide URI for a comparison genomesused to make the PAF"> + <repeat name="refgenomes" title="PAF reference comparison genome URI"> <param label="@LABEL@" name="annotation" type="text" /> <param label="Short name for track display" name="annoname" type="text" > <sanitizer invalid_char="_"> |