| Previous changeset 62:ab0d6782a95f (2024-03-28) Next changeset 64:497fd2d27aa2 (2024-03-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976 |
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modified:
jbrowse2.py jbrowse2.xml |
| b |
| diff -r ab0d6782a95f -r ac00dcfb5d1d jbrowse2.py --- 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"): |
| b |
| diff -r ab0d6782a95f -r ac00dcfb5d1d jbrowse2.xml --- a/jbrowse2.xml Thu Mar 28 04:51:06 2024 +0000 +++ b/jbrowse2.xml Thu Mar 28 07:46:04 2024 +0000 |
| b |
| b'@@ -541,7 +541,7 @@\n <assert_contents>\n <has_text text="genome path="></has_text>\n <has_text text="label="></has_text>\n- <has_text text="format="></has_text>\n+ <has_text text="useuri="></has_text>\n <has_text text="metadata"></has_text>\n </assert_contents>\n </output>\n@@ -576,7 +576,7 @@\n <has_text text="metadata"></has_text>\n <has_text text="useuri="></has_text>\n <has_text text="trackFile path="></has_text>\n- <has_text text="ext="bed" label="test-3.bed""></has_text>\n+ <has_text text="ext="vcf" label="merlin.vcf""></has_text>\n </assert_contents>\n </output>\n </test>\n@@ -588,7 +588,7 @@\n <param name="genome.ext" value="fasta"/>\n <param name="genome.name" value="Merlin"/>\n </conditional>\n- <repeat name="track_groups">\n+ <repeat name="track_groups">\n <param name="category" value="Default" />\n <repeat name="data_tracks">\n <conditional name="data_format">\n@@ -611,11 +611,9 @@\n </section>\n </repeat>\n </repeat>\n- </repeat>\n-\n- <repeat name="track_groups">\n+ <repeat name="track_groups">\n <param name="category" value="Ignore Scale" />\n- <repeat name="data_tracks">\n+ <repeat name="data_tracks">\n <conditional name="data_format">\n <param name="data_format_select" value="gff"/>\n <conditional name="useuri">\n@@ -635,150 +633,148 @@\n </conditional>\n </section>\n </conditional>\n+ </repeat>\n </repeat>\n- </repeat>\n-\n- <repeat name="track_groups">\n+ <repeat name="track_groups">\n <param name="category" value="Scaled Colour" />\n- <repeat name="data_tracks">\n- <conditional name="data_format">\n- <param name="data_format_select" value="gff"/>\n- <conditional name="useuri">\n- <param name="insource" value= "history"/>\n- <param name="annotation" value="gff3/C.gff"/>\n- </conditional>\n- <conditional name="match_part">\n- <param name="match_part_select" value="false"/>\n- </conditional>\n- <section name="jbcolor_scale">\n- <conditional name="color_score">\n- <param name="color_score_select" value="score"/>\n- <param name="score_scaling" value="linear"/>\n- <conditional name="score_scales">\n- <param name="scale_select" value="automatic"/>\n- </conditional>\n- <conditional name="color_scheme">\n- <param name="score_scheme" value="opacity"/>\n- <conditional name="color">\n- <param name="color_select" value="automatic"/>\n+ <repeat name="data_tracks">\n+ <conditional name="data_format">\n+ <param name="data_format_select" value="gff"/>\n+ <conditional name="useuri">\n+ <param name="insource" value= "history"/>\n+ <param name="annotation"'..b' <repeat name="data_tracks">\n- <conditional name="data_format">\n- <param name="data_format_select" value="gff"/>\n- <conditional name="useuri">\n- <param name="annotation" value="gff3/1.gff"/>\n- <param name="insource" value= "history"/>\n- </conditional>\n- <conditional name="match_part">\n- <param name="match_part_select" value="false"/>\n- </conditional>\n- <section name="jbcolor_scale">\n- <conditional name="color_score">\n- <param name="color_score_select" value="none"/>\n- </conditional>\n- <conditional name="color">\n- <param name="color_select" value="automatic"/>\n- </conditional>\n- </section>\n- <section name="jbmenu">\n- <repeat name="track_menu">\n- <param name="menu_action" value="iframeDialog"/>\n- <param name="menu_label" value="Some menu item"/>\n- <param name="menu_title" value="Frame title"/>\n- <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/>\n- <param name="menu_icon" value="dijitIconNewTask"/>\n- </repeat>\n- <repeat name="track_menu">\n- <param name="menu_action" value="newWindow"/>\n- <param name="menu_label" value="Another menu item"/>\n- <param name="menu_title" value="Frame title 2"/>\n- <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/>\n- </repeat>\n- </section>\n- </conditional>\n- </repeat>\n- <repeat name="data_tracks">\n- <conditional name="data_format">\n- <param name="data_format_select" value="gff"/>\n- <conditional name="useuri">\n- <param name="annotation" value="gff3/1.gff"/>\n- <param name="insource" value= "history"/>\n- </conditional>\n- <conditional name="match_part">\n- <param name="match_part_select" value="false"/>\n- </conditional>\n- <section name="jbcolor_scale">\n- <conditional name="color_score">\n- <param name="color_score_select" value="none"/>\n- </conditional>\n- <conditional name="color">\n- <param name="color_select" value="automatic"/>\n- </conditional>\n- </section>\n- </conditional>\n- </repeat>\n- </repeat>\n- </repeat>\n- <param name="uglyTestingHack" value="enabled" />\n- <output name="output">\n- <assert_contents>\n- <has_text text="With menu or index"/>\n- <has_text text="gff"/>\n- </assert_contents>\n- </output>\n- </test>\n+\n \n <!-- TODO add a synteny test -->\n <!-- TODO add a bam and a cram test -->\n' |