| Previous changeset 30:8f02a84ee278 (2024-02-21) Next changeset 32:fe48ed5810bd (2024-02-23) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty |
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modified:
jbrowse2.py jbrowse2.xml macros.xml |
| b |
| diff -r 8f02a84ee278 -r cb4b32ca9968 jbrowse2.py --- a/jbrowse2.py Wed Feb 21 02:57:30 2024 +0000 +++ b/jbrowse2.py Fri Feb 23 07:15:42 2024 +0000 |
| [ |
| @@ -450,22 +450,24 @@ if len(genome_name.split()) > 1: genome_name = genome_name.split()[0] # spaces and cruft break scripts when substituted - fapath = genome_node["path"] - assem = self.make_assembly(fapath, genome_name) - 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_firstcontig = None - fl = open(fapath, "r").readline().strip().split(">") - if len(fl) > 1: - fl = fl[1] - if len(fl.split()) > 1: - self.genome_firstcontig = fl.split()[0].strip() - else: - self.genome_firstcontig = fl + if genome_name not in self.genome_names: + # ignore dupes - can have multiple pafs with same references? + fapath = genome_node["path"] + assem = self.make_assembly(fapath, genome_name) + 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_firstcontig = None + fl = open(fapath, "r").readline().strip().split(">") + if len(fl) > 1: + fl = fl[1] + if len(fl.split()) > 1: + self.genome_firstcontig = fl.split()[0].strip() + else: + self.genome_firstcontig = fl if self.config_json.get("assemblies", None): self.config_json["assemblies"] += assemblies else: @@ -1013,26 +1015,31 @@ def add_paf(self, data, trackData, pafOpts, **kwargs): tname = trackData["name"] tId = trackData["label"] - pgname = pafOpts["genome_label"] - if len(pgname.split()) > 1: - pgname = pgname.split()[ - 0 - ] # trouble from spacey names in command lines avoidance - asstrack = self.make_assembly(pafOpts["genome"], pgname) - self.genome_names.append(pgname) - if self.config_json.get("assemblies", None): - self.config_json["assemblies"].append(asstrack) - else: - self.config_json["assemblies"] = [ - asstrack, - ] + 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] + # trouble from spacey names in command lines avoidance + if gname not in self.genome_names: + passnames.append(gname) + # ignore if already there - eg for duplicates among pafs. + asstrack = self.make_assembly(pgpaths[i], gname) + 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": [self.genome_name, pgname], + "assemblyNames": passnames, "name": tname, "adapter": { "type": "PAFAdapter", @@ -1533,6 +1540,9 @@ 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, |
| b |
| diff -r 8f02a84ee278 -r cb4b32ca9968 jbrowse2.xml --- a/jbrowse2.xml Wed Feb 21 02:57:30 2024 +0000 +++ b/jbrowse2.xml Fri Feb 23 07:15:42 2024 +0000 |
| [ |
| b'@@ -17,9 +17,12 @@\n python \'$__tool_directory__/jbrowse2.py\'\n --outdir \'$output.files_path\'\n --xml \'$trackxml\' &&\n-\n-cp \'$output.files_path/index.html\' \'$output\'\n-\n+#if $jbgen.zipOut == "true":\n+ (cd \'$output.files_path\' && zip -r - . ) > JBrowse2.zip &&\n+ mv JBrowse2.zip \'$output\'\n+#else\n+ cp \'$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@@ -77,6 +80,7 @@\n </genomes>\n <general>\n <defaultLocation>${jbgen.defaultLocation}</defaultLocation>\n+ <zipOut>${jbgen.zipOut}</zipOut>\n <analytics>${jbgen.enableAnalytics}</analytics>\n <primary_color>${jbgen.primary_color}</primary_color>\n <secondary_color>${jbgen.secondary_color}</secondary_color>\n@@ -89,100 +93,109 @@\n </metadata>\n <tracks>\n #for $tg in $track_groups:\n- #for $track in $tg.data_tracks:\n- <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n- #if $track.data_format.data_format_select != "sparql":\n- <files>\n- #set dataset = $track.data_format.annotation\n- <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">\n- <metadata>\n- <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"\n- size="${dataset.get_size(nice_size=True)}"\n- edam_format="${dataset.datatype.edam_format}"\n- file_ext="${dataset.ext}" />\n- <history id="${__app__.security.encode_id($dataset.history_id)}"\n- #if $dataset.history.user:\n- user_email="${dataset.history.user.email}"\n- user_id="${dataset.history.user_id}"\n- display_name="${dataset.history.get_display_name()}"/>\n- #else\n- user_email="anonymous"\n- user_id="-1"\n- display_name="Unnamed History"/>\n- #end if\n- <metadata\n- #for (key, value) in $dataset.get_metadata().items():\n- #if "_types" not in $key and $value is not None and len(str($value)) < 5000:\n- #if isinstance($value, list):\n- #set value_str = "[%s]" % \',\'.join([str(val) for val in value])\n- ${key}="$value_str"\n- #else\n- ${key}="${value}"\n- #end if\n- #end if\n- #end for\n- />\n- <tool\n- tool_id="${dataset.creating_job.tool_id}"\n- tool_version="${dataset.creating_job.tool_version}"\n- />\n- </metadata>\n- </trackFile>\n- </files>\n- #end if\n+ #for $track in $tg.data_tracks:\n+ <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n+ #if $track.data_format.data_format_select != "sparql":\n+ <files>\n+ #set dataset = $track.data_format.annotation\n+ <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">\n+ <metadata>\n+ <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"\n+ size="${dataset.get_size(nice_size=True)}"\n+ edam_format="${dataset.datatype.edam_format}"\n+ file_ext="${dataset.ext}" />\n+ <history id="${__ap'..b'$gnome,\n+ #end for\n+ </genome>\n+ <genome_label>\n+ #for gnome in $track.data_format.synteny_genome:\n+ $gnome.name,\n+ #end for\n+ </genome_label>\n+ </paf>\n+ #else if str($track.data_format.data_format_select) == "hic":\n+ <hic>\n+ </hic>\n+ #else if str($track.data_format.data_format_select) == "cool":\n+ <cool>\n+ </cool>\n+ #else if str($track.data_format.data_format_select) == "sparql":\n+ <label>${track.data_format.label}</label>\n+ <sparql>\n+ <url>${track.data_format.url}</url>\n+ <query>${track.data_format.query}</query>\n+ <query_refnames>${track.data_format.query_refnames}</query_refnames>\n+ </sparql>\n+ #end if\n+ </options>\n+ </track>\n #end for\n- #end for\n+ #end for\n </tracks>\n </root>\n ]]></configfile>\n@@ -236,7 +249,7 @@\n <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>\n <option value="paf">PAF - approximate mapping positions between two set of sequences</option>\n <option value="sparql">SPARQL</option>\n- <option value="vcf">VCF SNP annotation</option>\n+ <option value="vcf">VCF SNP</option>\n </param>\n <when value="blast">\n <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />\n@@ -302,11 +315,12 @@\n <expand macro="track_visibility" />\n </when>\n <when value="paf">\n- <param label="Comparison genome sequence" help="Paf from this as the reference, using the real reference as the reads to map"\n+ <param label="Comparison genome sequence" help="Paf from these as the references, using the real reference as the reads to map"\n format="fasta"\n name="synteny_genome"\n- type="data" />\n- <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/>\n+ type="data"\n+ multiple="True"/>\n+ <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/>\n <expand macro="track_visibility" />\n </when>\n \n@@ -376,7 +390,11 @@\n <param type="hidden" name="uglyTestingHack" value="" />\n </inputs>\n <outputs>\n- <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name"/>\n+ <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name">\n+ <change_format>\n+ <when input="zipOut" value="true" format="zip" />\n+ </change_format>\n+ </data>\n </outputs>\n <tests>\n <test>\n@@ -405,6 +423,7 @@\n </assert_contents>\n </output>\n </test>\n+\n <test>\n <param name="reference_genome|genome_type_select" value="history"/>\n <param name="reference_genome|genome" value="merlin.fa"/>\n@@ -739,6 +758,7 @@\n </assert_contents>\n </output>\n </test>\n+\n <!-- TODO add a synteny test -->\n <!-- TODO add a bam and a cram test -->\n <!-- TODO add an hic test -->\n' |
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| diff -r 8f02a84ee278 -r cb4b32ca9968 macros.xml --- a/macros.xml Wed Feb 21 02:57:30 2024 +0000 +++ b/macros.xml Fri Feb 23 07:15:42 2024 +0000 |
| [ |
| @@ -140,6 +140,8 @@ <xml name="general_options"> <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> + <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" /> @@ -502,7 +504,6 @@ </sanitizer> </xml> - <xml name="input_conditional" token_label="Track Data" token_format="data"> <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="False"/> </xml> |