| Previous changeset 88:efd1d41f11b4 (2024-04-14) Next changeset 90:51980e0dafd2 (2024-04-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 |
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modified:
jbrowse2.py jbrowse2.xml macros.xml test-data/jbrowse2_result02.zip |
| b |
| diff -r efd1d41f11b4 -r 408781c080fc jbrowse2.py --- a/jbrowse2.py Sun Apr 14 03:49:10 2024 +0000 +++ b/jbrowse2.py Wed Apr 17 22:18:47 2024 +0000 |
| [ |
| b'@@ -21,7 +21,8 @@\n \n JB2VER = "v2.10.3"\n # version pinned if cloning - but not cloning now\n-\n+logCommands = True\n+# useful for seeing what\'s being written but not for production setups\n TODAY = datetime.datetime.now().strftime("%Y-%m-%d")\n SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))\n GALAXY_INFRASTRUCTURE_URL = None\n@@ -427,14 +428,19 @@\n \n def subprocess_check_call(self, command, output=None, cwd=True):\n if output:\n- log.debug("cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output)\n+ if logCommands:\n+ log.debug(\n+ "cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output\n+ )\n subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output)\n else:\n- log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command))\n+ if logCommands:\n+ log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command))\n subprocess.check_call(command, cwd=self.get_cwd(cwd))\n \n def subprocess_popen(self, command, cwd=True):\n- log.debug(command)\n+ if logCommands:\n+ log.debug(command)\n p = subprocess.Popen(\n command,\n cwd=self.get_cwd(cwd),\n@@ -452,7 +458,8 @@\n raise RuntimeError("Command failed with exit code %s" % (retcode))\n \n def subprocess_check_output(self, command):\n- log.debug(" ".join(command))\n+ if logCommands:\n+ log.debug(" ".join(command))\n return subprocess.check_output(command, cwd=self.outdir)\n \n def symlink_or_copy(self, src, dest):\n@@ -491,14 +498,14 @@\n nrow = len(fl)\n except Exception:\n nrow = 0\n- logging.debug("### getNrow returning %d" % nrow)\n+ logging.debug("### getNrow %s returning %d" % (url, nrow))\n return nrow\n \n def process_genomes(self, genomes):\n assembly = []\n assmeta = []\n useuri = False\n- genome_names = []\n+ primaryGenome = None\n for i, genome_node in enumerate(genomes):\n this_genome = {}\n if genome_node["useuri"] == "yes":\n@@ -509,17 +516,18 @@\n if len(genome_name.split()) > 1:\n genome_name = genome_name.split()[0]\n # spaces and cruft break scripts when substituted\n- if genome_name not in genome_names:\n- # pafs with shared references\n+ if not primaryGenome:\n+ primaryGenome = genome_name\n+ if genome_name not in self.genome_names:\n+ self.genome_names.append(genome_name)\n fapath = genome_node["path"]\n if not useuri:\n fapath = os.path.realpath(fapath)\n assem, first_contig = self.make_assembly(fapath, genome_name, useuri)\n assembly.append(assem)\n self.ass_first_contigs.append(first_contig)\n- if len(genome_names) == 0:\n+ if genome_name == primaryGenome: # first one\n this_genome["genome_name"] = genome_name # first one for all tracks\n- genome_names.append(genome_name)\n this_genome["genome_sequence_adapter"] = assem["sequence"][\n "adapter"\n ]\n@@ -551,10 +559,9 @@\n )\n assmeta.append(this_genome)\n self.assemblies += assembly\n- self.assmeta[genome_names[0]] = assmeta\n- self.tracksToAdd[genome_names[0]] = []\n- self.genome_names += genome_names\n- return this_genome["genome_name"]\n+ self.assmeta[primaryGenome] = assmeta\n+ self.tracksToAdd[primaryGenome] = []\n+ return primaryGenome\n \n def make_assembly(self, fapath, gname, useuri):\n """added code to grab the first contig name and length for broken default session from Anthony and Helena\'s c'..b' os.path.realpath(x.attrib["path"]),\n x.attrib["ext"],\n x.attrib["useuri"],\n- x.attrib["label"],\n+ track_conf["label"],\n metadata,\n )\n track_conf["trackfiles"].append(tfa)\n@@ -1714,14 +1717,13 @@\n track_conf["format"] = track.attrib["format"]\n track_conf["conf"] = etree_to_dict(track.find("options"))\n keys = jc.process_annotations(track_conf)\n-\n if keys:\n for key in keys:\n vis = track.attrib.get("visibility", "default_off")\n if not vis:\n vis = "default_off"\n- default_session_data[assref_name]["visibility"][vis].append(key)\n- trakdat = jc.tracksToAdd[assref_name]\n+ default_session_data[primaryGenome]["visibility"][vis].append(key)\n+ trakdat = jc.tracksToAdd[primaryGenome]\n stile = {}\n for trak in trakdat:\n if trak["trackId"] == key:\n@@ -1732,21 +1734,20 @@\n for item in track.find("options/style")\n }\n stile.update(supdate)\n- default_session_data[assref_name]["style"][key] = stile\n- logging.debug("@@@ for %s got style=%s" % (key, stile))\n+ default_session_data[primaryGenome]["style"][key] = stile\n if track.find("options/style_labels"):\n- default_session_data[assref_name]["style_labels"][key] = {\n+ default_session_data[primaryGenome]["style_labels"][key] = {\n item.tag: parse_style_conf(item)\n for item in track.find("options/style_labels")\n }\n- default_session_data[assref_name]["tracks"].append(key)\n+ default_session_data[primaryGenome]["tracks"].append(key)\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- logging.debug("default_session=%s" % (default_session_data))\n+ logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))\n jc.zipOut = root.find("metadata/general/zipOut").text == "true"\n general_data = {\n "analytics": root.find("metadata/general/analytics").text,\n@@ -1759,12 +1760,28 @@\n jc.add_general_configuration(general_data)\n trackconf = jc.config_json.get("tracks", [])\n for gnome in jc.genome_names:\n- trackconf += jc.tracksToAdd[gnome]\n+ gtracks = jc.tracksToAdd[gnome]\n+ if len(gtracks) > 0:\n+ logging.debug(\n+ "for genome %s adding gtracks %s"\n+ % (gnome, json.dumps(gtracks, indent=2))\n+ )\n+ trackconf += gtracks\n jc.config_json["tracks"] = trackconf\n assconf = jc.config_json.get("assemblies", [])\n assconf += jc.assemblies\n jc.config_json["assemblies"] = assconf\n- logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names))\n+ logging.debug(\n+ "assmeta=%s, first_contigs=%s, assemblies=%s, gnames=%s, trackidlist=%s, tracks=%s"\n+ % (\n+ jc.assmeta,\n+ jc.ass_first_contigs,\n+ json.dumps(assconf, indent=2),\n+ jc.genome_names,\n+ jc.trackIdlist,\n+ json.dumps(trackconf, indent=2),\n+ )\n+ )\n jc.write_config()\n jc.add_default_session(default_session_data)\n # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.\n' |
| b |
| diff -r efd1d41f11b4 -r 408781c080fc jbrowse2.xml --- a/jbrowse2.xml Sun Apr 14 03:49:10 2024 +0000 +++ b/jbrowse2.xml Wed Apr 17 22:18:47 2024 +0000 |
| b |
| @@ -263,25 +263,15 @@ #if $track.data_format.pafuseuri.insource == "history": <genome> #for $anno in $track.data_format.pafuseuri.annotation: - ${anno}, + ${anno}:${anno.name}, #end for </genome> - <genome_label> - #for $anno in $track.data_format.pafuseuri.annotation: - ${anno.name}, - #end for - </genome_label> #else: <genome> #for $refgenome in $track.data_format.pafuseuri.refuri: - $refgenome.annotation, + ${refgenome.annotation}:${refgenome.annoname}, #end for </genome> - <genome_label> - #for $refgenome in $track.data_format.pafuseuri.refuri: - ${refgenome.annoname}, - #end for - </genome_label> #end if </paf> #else if str($track.data_format.data_format_select) == "hic": @@ -477,7 +467,7 @@ <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> - <data format="html" name="output" label="JBrowse2"> + <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}"> <change_format> <when input="zipOut" value="true" format="zip" /> </change_format> @@ -643,6 +633,7 @@ </repeat> <section name="jbgen"> <param name="zipOut" value="true" /> + <param name="session_name" value="New test session"/> </section> <output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"> <assert_contents> @@ -656,25 +647,24 @@ <has_archive_member path="galaxy.xml"> <is_valid_xml /> <xml_element path="./metadata/general/session_name" n="1"> - <has_text_matching expression="New session"/> + <has_text_matching expression="New test session"/> <not_has_text text="Newton"/> </xml_element> </has_archive_member> - <has_archive_member path="merlin.gff3_0.gff3.gz"/> - <has_archive_member path="merlin.bw_1.bigwig"/> - <has_archive_member path="test-6.bed_2.bed.gz"/> - <has_archive_member path="merlin.vcf_3.vcf.tbi"/> - <has_archive_member path="merlin.cram_4.cram"/> - <has_archive_member path="merlin-sample.bam_5.bam"/> - <has_archive_member path="merlinlastz.maf_6.maf.sorted.bed.gz.tbi"/> - <has_archive_member path="merlin.blastxml_7.blastxml.gz"/> - <has_archive_member path="dm3test.cool_9.cool.hic"/> - <has_archive_member path="peach-grape-map.paf_10.paf"/> + <has_archive_member path="merlin.gff3_0.gz"/> + <has_archive_member path="merlin.bw_1"/> + <has_archive_member path="test-6.bed_2.gz"/> + <has_archive_member path="merlin.vcf_3.tbi"/> + <has_archive_member path="merlin.cram_4"/> + <has_archive_member path="merlin-sample.bam_5"/> + <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/> + <has_archive_member path="merlin.blastxml_7.gz"/> + <has_archive_member path="dm3test.cool_9.hic"/> + <has_archive_member path="peach-grape-map.paf_10"/> <has_archive_member path="Merlin.fa.gz.fai"/> <has_archive_member path="config.json"> <has_json_property_with_text property="name" text="Merlin" /> </has_archive_member> - </assert_contents> </output> </test> |
| b |
| diff -r efd1d41f11b4 -r 408781c080fc macros.xml --- a/macros.xml Sun Apr 14 03:49:10 2024 +0000 +++ b/macros.xml Wed Apr 17 22:18:47 2024 +0000 |
| [ |
| @@ -28,8 +28,8 @@ <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. +This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is +maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own. ]]> </token> <xml name="genome_selector" @@ -157,7 +157,7 @@ <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="Session name" type="text" name="session_name" value="New JB2 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"> |
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| diff -r efd1d41f11b4 -r 408781c080fc test-data/jbrowse2_result02.zip |
| b |
| Binary file test-data/jbrowse2_result02.zip has changed |