Mercurial > repos > fubar > jbrowse2
changeset 31:cb4b32ca9968 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
| author | fubar |
|---|---|
| date | Fri, 23 Feb 2024 07:15:42 +0000 |
| parents | 8f02a84ee278 |
| children | fe48ed5810bd |
| files | jbrowse2.py jbrowse2.xml macros.xml |
| diffstat | 3 files changed, 161 insertions(+), 130 deletions(-) [+] |
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--- 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,
--- a/jbrowse2.xml Wed Feb 21 02:57:30 2024 +0000 +++ b/jbrowse2.xml Fri Feb 23 07:15:42 2024 +0000 @@ -17,9 +17,12 @@ python '$__tool_directory__/jbrowse2.py' --outdir '$output.files_path' --xml '$trackxml' && - -cp '$output.files_path/index.html' '$output' - +#if $jbgen.zipOut == "true": + (cd '$output.files_path' && zip -r - . ) > JBrowse2.zip && + mv JBrowse2.zip '$output' +#else + cp '$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' @@ -77,6 +80,7 @@ </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> @@ -89,100 +93,109 @@ </metadata> <tracks> #for $tg in $track_groups: - #for $track in $tg.data_tracks: - <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> - #if $track.data_format.data_format_select != "sparql": - <files> - #set dataset = $track.data_format.annotation - <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> - <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> - </files> - #end if + #for $track in $tg.data_tracks: + <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> + #if $track.data_format.data_format_select != "sparql": + <files> + #set dataset = $track.data_format.annotation + <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> + <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> + </files> + #else + <track cat="${tg.category}" format="sparql" visibility="off"> + #end if - <options> - + <options> - #if str($track.data_format.data_format_select) == "pileup": - <pileup> - <bam_indices> - <bam_index>${dataset.metadata.bam_index}</bam_index> - </bam_indices> - </pileup> - #else if str($track.data_format.data_format_select) == "cram": - <cram> - <cram_indices> - <cram_index>${dataset.metadata.cram_index}</cram_index> - </cram_indices> - </cram> - #else if str($track.data_format.data_format_select) == "blast": - <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) == "gene_calls": - <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($track.data_format.data_format_select) == "paf": - <paf> - <genome>${track.data_format.synteny_genome}</genome> - <genome_label>${track.data_format.synteny_genome.name}</genome_label> - </paf> - #else if str($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) == "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> + #if str($track.data_format.data_format_select) == "pileup": + <pileup> + <bam_indices> + <bam_index>${dataset.metadata.bam_index}</bam_index> + </bam_indices> + </pileup> + #else if str($track.data_format.data_format_select) == "cram": + <cram> + <cram_indices> + <cram_index>${dataset.metadata.cram_index}</cram_index> + </cram_indices> + </cram> + #else if str($track.data_format.data_format_select) == "blast": + <blast> + #if str($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) == "gene_calls": + <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) == "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 for - #end for + #end for </tracks> </root> ]]></configfile> @@ -236,7 +249,7 @@ <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="sparql">SPARQL</option> - <option value="vcf">VCF SNP annotation</option> + <option value="vcf">VCF SNP</option> </param> <when value="blast"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> @@ -302,11 +315,12 @@ <expand macro="track_visibility" /> </when> <when value="paf"> - <param label="Comparison genome sequence" help="Paf from this as the reference, using the real reference as the reads to map" + <param label="Comparison genome sequence" help="Paf from these as the references, using the real reference as the reads to map" format="fasta" name="synteny_genome" - type="data" /> - <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/> + 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_visibility" /> </when> @@ -376,7 +390,11 @@ <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> - <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name"/> + <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name"> + <change_format> + <when input="zipOut" value="true" format="zip" /> + </change_format> + </data> </outputs> <tests> <test> @@ -405,6 +423,7 @@ </assert_contents> </output> </test> + <test> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> @@ -739,6 +758,7 @@ </assert_contents> </output> </test> + <!-- TODO add a synteny test --> <!-- TODO add a bam and a cram test --> <!-- TODO add an hic test -->
--- 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>