Mercurial > repos > fubar > jbrowse2
changeset 34:2893ef33fba9 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
| author | fubar |
|---|---|
| date | Sun, 25 Feb 2024 04:18:53 +0000 |
| parents | 9aedb7f1cc77 |
| children | 15da358c3108 |
| files | jbrowse2.py jbrowse2.xml more |
| diffstat | 3 files changed, 75 insertions(+), 20 deletions(-) [+] |
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--- a/jbrowse2.py Sat Feb 24 10:44:01 2024 +0000 +++ b/jbrowse2.py Sun Feb 25 04:18:53 2024 +0000 @@ -17,7 +17,7 @@ logging.basicConfig(level=logging.INFO) log = logging.getLogger("jbrowse") -JB2VER = "v2.10.1" +JB2VER = "v2.10.2" # version pinned for cloning TODAY = datetime.datetime.now().strftime("%Y-%m-%d") @@ -450,7 +450,7 @@ if len(genome_name.split()) > 1: genome_name = genome_name.split()[0] # spaces and cruft break scripts when substituted - if genome_name not in self.genome_names: + 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) @@ -1015,16 +1015,16 @@ def add_paf(self, data, trackData, pafOpts, **kwargs): tname = trackData["name"] tId = trackData["label"] - 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 + 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. + # 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): @@ -1126,7 +1126,7 @@ # Unsanitize labels (element_identifiers are always sanitized by Galaxy) for key, value in mapped_chars.items(): track_human_label = track_human_label.replace(value, key) - track_human_label = track_human_label.replace(" ","_") + track_human_label = track_human_label.replace(" ", "_") outputTrackConfig = { "category": category, "style": {}, @@ -1149,7 +1149,7 @@ dataset_ext, outputTrackConfig, ) - elif dataset_ext in ("hic","juicebox_hic"): + elif dataset_ext in ("hic", "juicebox_hic"): self.add_hic( dataset_path, outputTrackConfig, @@ -1540,9 +1540,7 @@ default_session_data["session_name"] = root.find( "metadata/general/session_name" ).text - jc.zipOut = root.find( - "metadata/general/zipOut" - ).text == "true" + 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 Sat Feb 24 10:44:01 2024 +0000 +++ b/jbrowse2.xml Sun Feb 25 04:18:53 2024 +0000 @@ -1,4 +1,4 @@ - <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_4" profile="22.05"> + <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" profile="22.05"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -18,8 +18,7 @@ --outdir '$output.files_path' --xml '$trackxml' && #if $jbgen.zipOut == "true": - (cd '$output.files_path' && zip -r - . ) > JBrowse2.zip && - mv JBrowse2.zip '$output' + (cd '$output.files_path' && zip -r - . ) > '$output' #else cp '$output.files_path/index.html' '$output' #end if @@ -471,7 +470,7 @@ <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gene_calls"/> - <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/> + <param name="annotation" value="bed/test-3.bed"/> </conditional> </repeat> </repeat> @@ -496,7 +495,7 @@ <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gene_calls"/> - <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> + <param name="annotation" value="gff3/A.gff"/> <conditional name="match_part"> <param name="match_part_select" value="false"/> </conditional> @@ -539,7 +538,7 @@ <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gene_calls"/> - <param name="annotation" value="gff3/1.gff"/> + <param name="annotation" value="gff3/C.gff"/> <conditional name="match_part"> <param name="match_part_select" value="false"/> </conditional> @@ -563,7 +562,7 @@ <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gene_calls"/> - <param name="annotation" value="gff3/1.gff"/> + <param name="annotation" value="gff3/B.gff"/> <conditional name="match_part"> <param name="match_part_select" value="false"/> </conditional> @@ -588,7 +587,7 @@ <repeat name="data_tracks"> <conditional name="data_format"> <param name="data_format_select" value="gene_calls"/> - <param name="annotation" value="gff3/1.gff"/> + <param name="annotation" value="gff3/A.gff"/> <conditional name="match_part"> <param name="match_part_select" value="false"/> </conditional> @@ -686,7 +685,7 @@ <has_text text="A.gff"/> <has_text text="B.gff"/> <has_text text="C.gff"/> - <has_text text="D.gff"/> + <has_text text="interpro.gff"/> <has_text text="Scaled Colour"/> <has_text text="1.gff"/> <has_text text="2.gff"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/more Sun Feb 25 04:18:53 2024 +0000 @@ -0,0 +1,58 @@ +jbrowse2.py:2:80: E501 line too long (94 > 79 characters) +jbrowse2.py:84:80: E501 line too long (124 > 79 characters) +jbrowse2.py:85:80: E501 line too long (83 > 79 characters) +jbrowse2.py:88:80: E501 line too long (83 > 79 characters) +jbrowse2.py:102:80: E501 line too long (86 > 79 characters) +jbrowse2.py:234:80: E501 line too long (87 > 79 characters) +jbrowse2.py:261:80: E501 line too long (84 > 79 characters) +jbrowse2.py:266:80: E501 line too long (84 > 79 characters) +jbrowse2.py:267:80: E501 line too long (85 > 79 characters) +jbrowse2.py:275:80: E501 line too long (85 > 79 characters) +jbrowse2.py:283:80: E501 line too long (85 > 79 characters) +jbrowse2.py:295:80: E501 line too long (84 > 79 characters) +jbrowse2.py:348:80: E501 line too long (87 > 79 characters) +jbrowse2.py:351:80: E501 line too long (83 > 79 characters) +jbrowse2.py:357:80: E501 line too long (107 > 79 characters) +jbrowse2.py:367:80: E501 line too long (118 > 79 characters) +jbrowse2.py:392:80: E501 line too long (82 > 79 characters) +jbrowse2.py:461:80: E501 line too long (80 > 79 characters) +jbrowse2.py:554:80: E501 line too long (101 > 79 characters) +jbrowse2.py:558:80: E501 line too long (90 > 79 characters) +jbrowse2.py:560:80: E501 line too long (94 > 79 characters) +jbrowse2.py:562:80: E501 line too long (94 > 79 characters) +jbrowse2.py:563:80: E501 line too long (123 > 79 characters) +jbrowse2.py:597:80: E501 line too long (133 > 79 characters) +jbrowse2.py:605:80: E501 line too long (124 > 79 characters) +jbrowse2.py:624:80: E501 line too long (87 > 79 characters) +jbrowse2.py:783:80: E501 line too long (81 > 79 characters) +jbrowse2.py:784:80: E501 line too long (97 > 79 characters) +jbrowse2.py:790:80: E501 line too long (102 > 79 characters) +jbrowse2.py:791:80: E501 line too long (101 > 79 characters) +jbrowse2.py:792:80: E501 line too long (99 > 79 characters) +jbrowse2.py:794:80: E501 line too long (84 > 79 characters) +jbrowse2.py:830:80: E501 line too long (83 > 79 characters) +jbrowse2.py:831:80: E501 line too long (93 > 79 characters) +jbrowse2.py:837:80: E501 line too long (102 > 79 characters) +jbrowse2.py:838:80: E501 line too long (101 > 79 characters) +jbrowse2.py:839:80: E501 line too long (99 > 79 characters) +jbrowse2.py:841:80: E501 line too long (86 > 79 characters) +jbrowse2.py:843:80: E501 line too long (81 > 79 characters) +jbrowse2.py:925:80: E501 line too long (82 > 79 characters) +jbrowse2.py:1126:80: E501 line too long (84 > 79 characters) +jbrowse2.py:1193:80: E501 line too long (81 > 79 characters) +jbrowse2.py:1206:80: E501 line too long (80 > 79 characters) +jbrowse2.py:1243:80: E501 line too long (146 > 79 characters) +jbrowse2.py:1245:80: E501 line too long (83 > 79 characters) +jbrowse2.py:1260:80: E501 line too long (123 > 79 characters) +jbrowse2.py:1295:80: E501 line too long (107 > 79 characters) +jbrowse2.py:1301:80: E501 line too long (106 > 79 characters) +jbrowse2.py:1309:80: E501 line too long (80 > 79 characters) +jbrowse2.py:1314:80: E501 line too long (87 > 79 characters) +jbrowse2.py:1347:80: E501 line too long (82 > 79 characters) +jbrowse2.py:1354:80: E501 line too long (80 > 79 characters) +jbrowse2.py:1408:80: E501 line too long (86 > 79 characters) +jbrowse2.py:1432:80: E501 line too long (117 > 79 characters) +jbrowse2.py:1494:80: E501 line too long (94 > 79 characters) +jbrowse2.py:1504:80: E501 line too long (88 > 79 characters) +jbrowse2.py:1517:80: E501 line too long (86 > 79 characters) +jbrowse2.py:1549:80: E501 line too long (80 > 79 characters)