Mercurial > repos > fubar > jbrowse2
changeset 63:ac00dcfb5d1d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
| author | fubar |
|---|---|
| date | Thu, 28 Mar 2024 07:46:04 +0000 |
| parents | ab0d6782a95f |
| children | 497fd2d27aa2 |
| files | jbrowse2.py jbrowse2.xml |
| diffstat | 2 files changed, 140 insertions(+), 219 deletions(-) [+] |
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--- a/jbrowse2.py Thu Mar 28 04:51:06 2024 +0000 +++ b/jbrowse2.py Thu Mar 28 07:46:04 2024 +0000 @@ -15,7 +15,7 @@ import xml.etree.ElementTree as ET from collections import defaultdict -logging.basicConfig(level=logging.DEBUG) +logging.basicConfig(level=logging.INFO) log = logging.getLogger("jbrowse") JB2VER = "v2.10.3" @@ -493,7 +493,7 @@ else: try: fl = urllib.request.urlopen(fapath + ".fai").readline() - except: + except Exception: fl = None if fl: # is first row of the text fai so the first contig name this_genome["genome_firstcontig"] = ( @@ -622,7 +622,6 @@ # can be served - if public. # dsId = trackData["metadata"]["dataset_id"] # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) - hic_path = trackData.get("hic_path", None) useuri = trackData["useuri"].lower() == "yes" if useuri: uri = data @@ -682,7 +681,7 @@ sampu = list(dict.fromkeys(samp)) samples = [x.split(".")[0] for x in sampu] samples.sort() - logging.warn( + logging.debug( "$$$$ cmd=%s, mafss=%s samp=%s samples=%s" % (" ".join(cmd), mafss, samp, samples) ) @@ -737,7 +736,7 @@ ] subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) gff3_unrebased.close() - logging.warn("### blastxml to gff3 cmd = %s" % " ".join(cmd)) + logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd)) return gff3_unrebased.name def add_blastxml(self, data, trackData, blastOpts, **kwargs): @@ -749,7 +748,7 @@ cmd.append("--protein2dna") cmd.extend([os.path.realpath(blastOpts["parent"]), gff3]) subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) - logging.warn("### gff3rebase cmd = %s" % " ".join(cmd)) + logging.debug("### gff3rebase cmd = %s" % " ".join(cmd)) gff3_rebased.close() # Replace original gff3 file shutil.copy(gff3_rebased.name, gff3) @@ -1307,7 +1306,7 @@ track_types[tId] = track_conf["type"] style_data = default_data["style"].get(tId, None) if not style_data: - logging.warn( + logging.debug( "### No style data in default data %s for %s" % (default_data, tId) ) @@ -1488,7 +1487,6 @@ } for x in ass.findall("metadata/genomes/genome") ] - logging.warn("#!!! genomes=%s" % genomes) assref_name = jc.process_genomes(genomes) for track in ass.find("tracks"):
--- a/jbrowse2.xml Thu Mar 28 04:51:06 2024 +0000 +++ b/jbrowse2.xml Thu Mar 28 07:46:04 2024 +0000 @@ -541,7 +541,7 @@ <assert_contents> <has_text text="genome path="></has_text> <has_text text="label="></has_text> - <has_text text="format="></has_text> + <has_text text="useuri="></has_text> <has_text text="metadata"></has_text> </assert_contents> </output> @@ -576,7 +576,7 @@ <has_text text="metadata"></has_text> <has_text text="useuri="></has_text> <has_text text="trackFile path="></has_text> - <has_text text="ext="bed" label="test-3.bed""></has_text> + <has_text text="ext="vcf" label="merlin.vcf""></has_text> </assert_contents> </output> </test> @@ -588,7 +588,7 @@ <param name="genome.ext" value="fasta"/> <param name="genome.name" value="Merlin"/> </conditional> - <repeat name="track_groups"> + <repeat name="track_groups"> <param name="category" value="Default" /> <repeat name="data_tracks"> <conditional name="data_format"> @@ -611,11 +611,9 @@ </section> </repeat> </repeat> - </repeat> - - <repeat name="track_groups"> + <repeat name="track_groups"> <param name="category" value="Ignore Scale" /> - <repeat name="data_tracks"> + <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gff"/> <conditional name="useuri"> @@ -635,150 +633,148 @@ </conditional> </section> </conditional> + </repeat> </repeat> - </repeat> - - <repeat name="track_groups"> + <repeat name="track_groups"> <param name="category" value="Scaled Colour" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="insource" value= "history"/> - <param name="annotation" value="gff3/C.gff"/> - </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> - </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="score"/> - <param name="score_scaling" value="linear"/> - <conditional name="score_scales"> - <param name="scale_select" value="automatic"/> - </conditional> - <conditional name="color_scheme"> - <param name="score_scheme" value="opacity"/> - <conditional name="color"> - <param name="color_select" value="automatic"/> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="insource" value= "history"/> + <param name="annotation" value="gff3/C.gff"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="automatic"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> </conditional> </conditional> - </conditional> - </section> - </conditional> - </repeat> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/B.gff"/> - <param name="insource" value= "history"/> + </section> </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> - </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="score"/> - <param name="score_scaling" value="linear"/> - <conditional name="score_scales"> - <param name="scale_select" value="automatic"/> - </conditional> - <conditional name="color_scheme"> - <param name="score_scheme" value="opacity"/> - <conditional name="color"> - <param name="color_select" value="manual"/> - <param name="style_color" value="#0000ff"/> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/B.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="automatic"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="manual"/> + <param name="style_color" value="#0000ff"/> + </conditional> </conditional> </conditional> - </conditional> - </section> - </conditional> - </repeat> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/A.gff"/> - <param name="insource" value= "history"/> - </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> + </section> </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="score"/> - <param name="score_scaling" value="linear"/> - <conditional name="score_scales"> - <param name="scale_select" value="manual"/> - <param name="minimum" value="0"/> - <param name="maximum" value="1000"/> - </conditional> - <conditional name="color_scheme"> - <param name="score_scheme" value="opacity"/> - <conditional name="color"> - <param name="color_select" value="automatic"/> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/A.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="manual"/> + <param name="minimum" value="0"/> + <param name="maximum" value="1000"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> </conditional> </conditional> - </conditional> - </section> - </conditional> - </repeat> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/1.gff"/> - <param name="insource" value= "history"/> - </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> + </section> </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="score"/> - <param name="score_scaling" value="linear"/> - <conditional name="score_scales"> - <param name="scale_select" value="manual"/> - <param name="minimum" value="0"/> - <param name="maximum" value="1000"/> - </conditional> - <conditional name="color_scheme"> - <param name="score_scheme" value="opacity"/> - <conditional name="color"> - <param name="color_select" value="manual"/> - <param name="style_color" value="#ff0000"/> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/1.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="score"/> + <param name="score_scaling" value="linear"/> + <conditional name="score_scales"> + <param name="scale_select" value="manual"/> + <param name="minimum" value="0"/> + <param name="maximum" value="1000"/> + </conditional> + <conditional name="color_scheme"> + <param name="score_scheme" value="opacity"/> + <conditional name="color"> + <param name="color_select" value="manual"/> + <param name="style_color" value="#ff0000"/> + </conditional> </conditional> </conditional> - </conditional> - </section> - </conditional> - </repeat> - </repeat> - - <repeat name="track_groups"> - <param name="category" value="Realistic" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/interpro.gff"/> - <param name="insource" value= "history"/> + </section> </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> - </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="none"/> + </repeat> + </repeat> + <repeat name="track_groups"> + <param name="category" value="Realistic" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/interpro.gff"/> + <param name="insource" value= "history"/> </conditional> - <conditional name="color"> - <param name="color_select" value="automatic"/> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> </conditional> - </section> - </conditional> - </repeat> - <repeat name="data_tracks"> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gff"/> <conditional name="useuri"> @@ -798,13 +794,14 @@ </conditional> </section> </conditional> + </repeat> </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> - <has_text text="Auto Coloured"/> + <has_text text="Ignore Scale"/> <has_text text="A.gff"/> <has_text text="B.gff"/> <has_text text="C.gff"/> @@ -815,81 +812,7 @@ </assert_contents> </output> </test> - <test> - <repeat name="assemblies"> - <conditional name="reference_genome"> - <param name="genome_type_select" value="history"/> - <param name="genome" value="merlin.fa"/> - <param name="genome.ext" value="fasta"/> - <param name="genome.name" value="Merlin"/> - </conditional> - <repeat name="track_groups"> - <param name="category" value="Default" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/1.gff"/> - <param name="insource" value= "history"/> - </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> - </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="none"/> - </conditional> - <conditional name="color"> - <param name="color_select" value="automatic"/> - </conditional> - </section> - <section name="jbmenu"> - <repeat name="track_menu"> - <param name="menu_action" value="iframeDialog"/> - <param name="menu_label" value="Some menu item"/> - <param name="menu_title" value="Frame title"/> - <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> - <param name="menu_icon" value="dijitIconNewTask"/> - </repeat> - <repeat name="track_menu"> - <param name="menu_action" value="newWindow"/> - <param name="menu_label" value="Another menu item"/> - <param name="menu_title" value="Frame title 2"/> - <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> - </repeat> - </section> - </conditional> - </repeat> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/1.gff"/> - <param name="insource" value= "history"/> - </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> - </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="none"/> - </conditional> - <conditional name="color"> - <param name="color_select" value="automatic"/> - </conditional> - </section> - </conditional> - </repeat> - </repeat> - </repeat> - <param name="uglyTestingHack" value="enabled" /> - <output name="output"> - <assert_contents> - <has_text text="With menu or index"/> - <has_text text="gff"/> - </assert_contents> - </output> - </test> + <!-- TODO add a synteny test --> <!-- TODO add a bam and a cram test -->