| Previous changeset 32:6b774e9d6387 (2019-07-16) Next changeset 34:9de82b4963e6 (2019-09-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" |
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modified:
jbrowse.py jbrowse.xml macros.xml |
| b |
| diff -r 6b774e9d6387 -r 0ae74c70b267 jbrowse.py --- a/jbrowse.py Tue Jul 16 05:08:10 2019 -0400 +++ b/jbrowse.py Fri Aug 30 03:36:39 2019 -0400 |
| [ |
| b'@@ -331,13 +331,6 @@\n class JbrowseConnector(object):\n \n def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):\n- self.TN_TABLE = {\n- \'gff3\': \'--gff\',\n- \'gff\': \'--gff\',\n- \'bed\': \'--bed\',\n- \'genbank\': \'--gbk\',\n- }\n-\n self.cs = ColorScaling()\n self.jbrowse = jbrowse\n self.outdir = outdir\n@@ -379,9 +372,13 @@\n with open(trackList, \'w\') as handle:\n json.dump(trackListData, handle, indent=2)\n \n- def subprocess_check_call(self, command):\n- log.debug(\'cd %s && %s\', self.outdir, \' \'.join(command))\n- subprocess.check_call(command, cwd=self.outdir)\n+ def subprocess_check_call(self, command, output=None):\n+ if output:\n+ log.debug(\'cd %s && %s > %s\', self.outdir, \' \'.join(command), output)\n+ subprocess.check_call(command, cwd=self.outdir, stdout=output)\n+ else:\n+ log.debug(\'cd %s && %s\', self.outdir, \' \'.join(command))\n+ subprocess.check_call(command, cwd=self.outdir)\n \n def subprocess_popen(self, command):\n log.debug(\'cd %s && %s\', self.outdir, command)\n@@ -558,6 +555,41 @@\n \n self._add_track_json(trackData)\n \n+ def add_maf(self, data, trackData, mafOpts, **kwargs):\n+ script = os.path.realpath(os.path.join(self.jbrowse, \'plugins\', \'MAFViewer\', \'bin\', \'maf2bed.pl\'))\n+ dest = os.path.join(\'data\', \'raw\', trackData[\'label\'] + \'.txt\')\n+\n+ tmp1 = tempfile.NamedTemporaryFile(delete=False)\n+ tmp1.close()\n+\n+ # Process MAF to bed-like\n+ cmd = [script, data]\n+ self.subprocess_check_call(cmd, output=tmp1.path)\n+\n+ # Sort / Index it\n+ self._sort_bed(tmp1.path, dest)\n+ # Cleanup\n+ try:\n+ os.remove(tmp1.path)\n+ except OSError:\n+ pass\n+\n+ # Construct samples list\n+ # We could get this from galaxy metadata, not sure how easily.\n+ ps = subprocess.Popen([\'grep\', \'^s [^ ]*\', \'-o\', data], stdout=subprocess.PIPE)\n+ output = subprocess.check_output((\'sort\', \'-u\'), stdin=ps.stdout)\n+ ps.wait()\n+ samples = [x[2:] for x in output]\n+\n+ trackData.update({\n+ "storeClass": "MAFViewer/Store/SeqFeature/MAFTabix",\n+ "type": "MAFViewer/View/Track/MAF",\n+ "urlTemplate": trackData[\'label\'] + \'.txt.gz\',\n+ "samples": samples,\n+ })\n+\n+ self._add_track_json(trackData)\n+\n def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):\n dest = os.path.join(\'data\', \'raw\', trackData[\'label\'] + \'.bam\')\n cmd = [\'ln\', \'-s\', os.path.realpath(data), dest]\n@@ -610,19 +642,24 @@\n self._add_track_json(trackData)\n \n def _sort_gff(self, data, dest):\n-\n+ # Only index if not already done\n if not os.path.exists(dest):\n- # Only index if not already done\n cmd = "gff3sort.pl --precise \'%s\' | grep -v \\"^$\\" > \'%s\'" % (data, dest)\n self.subprocess_popen(cmd)\n \n- cmd = [\'bgzip\', \'-f\', dest]\n- self.subprocess_popen(\' \'.join(cmd))\n- cmd = [\'tabix\', \'-f\', \'-p\', \'gff\', dest + \'.gz\']\n- self.subprocess_popen(\' \'.join(cmd))\n+ self.subprocess_check_call([\'bgzip\', \'-f\', dest])\n+ self.subprocess_check_call([\'tabix\', \'-f\', \'-p\', \'gff\', dest + \'.gz\'])\n \n- def add_features(self, data, format, trackData, gffOpts, **kwargs):\n+ def _sort_bed(self, data, dest):\n+ # Only index if not already done\n+ if not os.path.exists(dest):\n+ cmd = [\'sort\', \'-k1,1\', \'-k2,2n\', data]\n+ self.subprocess_check_call(cmd, output=dest)\n \n+ self.subprocess_check_call([\'bgzip\', \'-f\', dest])\n+ self.subprocess_check_call([\'tabix\', \'-f\', \'-p\', \'bed\', dest + \'.gz\'])\n+\n+ def add_gff(self, data, format, trackData, gffOpts, **kwargs):\n dest = os.path.join(self.outdir, \'data\', \'raw\', trac'..b' trackData[\'topLevelFeatures\'] = gffOpts[\'topLevelFeatures\']\n+\n+ self._add_track_json(trackData)\n+\n+ if gffOpts.get(\'index\', \'false\') == \'true\':\n+ self.tracksToIndex.append("%s" % trackData[\'label\'])\n+\n+ def add_genbank(self, data, format, trackData, gffOpts, **kwargs):\n+ cmd = [\n+ \'perl\', self._jbrowse_bin(\'flatfile-to-json.pl\'),\n+ \'--genbank\', data,\n+ \'--trackLabel\', trackData[\'label\'],\n+ \'--key\', trackData[\'key\']\n+ ]\n+\n+ # className in --clientConfig is ignored, it needs to be set with --className\n+ if \'className\' in trackData[\'style\']:\n+ cmd += [\'--className\', trackData[\'style\'][\'className\']]\n+\n+ config = copy.copy(trackData)\n+ clientConfig = trackData[\'style\']\n+ del config[\'style\']\n+\n+ if \'match\' in gffOpts:\n+ config[\'glyph\'] = \'JBrowse/View/FeatureGlyph/Segments\'\n+ if bool(gffOpts[\'match\']):\n+ # Can be empty for CanvasFeatures = will take all by default\n+ cmd += [\'--type\', gffOpts[\'match\']]\n+\n+ cmd += [\'--clientConfig\', json.dumps(clientConfig)]\n+\n+ trackType = \'JBrowse/View/Track/CanvasFeatures\'\n+ if \'trackType\' in gffOpts:\n+ trackType = gffOpts[\'trackType\']\n+\n+ if trackType == \'JBrowse/View/Track/CanvasFeatures\':\n+ if \'transcriptType\' in gffOpts and gffOpts[\'transcriptType\']:\n+ config[\'transcriptType\'] = gffOpts[\'transcriptType\']\n+ if \'subParts\' in gffOpts and gffOpts[\'subParts\']:\n+ config[\'subParts\'] = gffOpts[\'subParts\']\n+ if \'impliedUTRs\' in gffOpts and gffOpts[\'impliedUTRs\']:\n+ config[\'impliedUTRs\'] = gffOpts[\'impliedUTRs\']\n+ elif trackType == \'JBrowse/View/Track/HTMLFeatures\':\n+ if \'transcriptType\' in gffOpts and gffOpts[\'transcriptType\']:\n+ cmd += [\'--type\', gffOpts[\'transcriptType\']]\n+\n+ cmd += [\n+ \'--trackType\', gffOpts[\'trackType\']\n+ ]\n+\n+ cmd.extend([\'--config\', json.dumps(config)])\n+\n+ self.subprocess_check_call(cmd)\n+\n+ if gffOpts.get(\'index\', \'false\') == \'true\':\n+ self.tracksToIndex.append("%s" % trackData[\'label\'])\n+\n def add_rest(self, url, trackData):\n data = {\n "label": trackData[\'label\'],\n@@ -782,15 +902,24 @@\n \n # import pprint; pprint.pprint(track)\n # import sys; sys.exit()\n- if dataset_ext in (\'gff\', \'gff3\', \'bed\'):\n- self.add_features(dataset_path, dataset_ext, outputTrackConfig,\n- track[\'conf\'][\'options\'][\'gff\'])\n+ if dataset_ext in (\'gff\', \'gff3\'):\n+ self.add_gff(dataset_path, dataset_ext, outputTrackConfig,\n+ track[\'conf\'][\'options\'][\'gff\'])\n+ elif dataset_ext in (\'bed\', ):\n+ self.add_bed(dataset_path, dataset_ext, outputTrackConfig,\n+ track[\'conf\'][\'options\'][\'gff\'])\n+ elif dataset_ext in (\'genbank\', ):\n+ self.add_genbank(dataset_path, dataset_ext, outputTrackConfig,\n+ track[\'conf\'][\'options\'][\'gff\'])\n elif dataset_ext == \'bigwig\':\n self.add_bigwig(dataset_path, outputTrackConfig,\n track[\'conf\'][\'options\'][\'wiggle\'])\n elif dataset_ext == \'bigwig_multiple\':\n self.add_bigwig_multiple(dataset_path, outputTrackConfig,\n track[\'conf\'][\'options\'][\'wiggle\'])\n+ elif dataset_ext == \'maf\':\n+ self.add_maf(dataset_path, outputTrackConfig,\n+ track[\'conf\'][\'options\'][\'maf\'])\n elif dataset_ext == \'bam\':\n real_indexes = track[\'conf\'][\'options\'][\'pileup\'][\'bam_indices\'][\'bam_index\']\n if not isinstance(real_indexes, list):\n' |
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| diff -r 6b774e9d6387 -r 0ae74c70b267 jbrowse.xml --- a/jbrowse.xml Tue Jul 16 05:08:10 2019 -0400 +++ b/jbrowse.xml Fri Aug 30 03:36:39 2019 -0400 |
| b |
| @@ -401,7 +401,7 @@ <repeat name="data_tracks" title="Annotation Track"> <conditional name="data_format" label="Track Options"> <param type="select" label="Track Type" name="data_format_select"> - <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> + <option value="gene_calls">GFF/GFF3/BED Features</option> <option value="pileup">BAM Pileups</option> <option value="blast">Blast XML</option> <option value="wiggle">BigWig XY</option> @@ -1167,14 +1167,14 @@ There are a few different types of tracks supported, each with their own set of options: -GFF3/BED/GBK -~~~~~~~~~~~~ +GFF3/BED +~~~~~~~~ These are your standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region. The underlying tool and this help documentation focus primarily on GFF3 data, and have not been tested extensively with other formats. Automatic -min/max detection will likely fail under BED and GBK datasets. +min/max detection will fail under BED datasets. The data may be of a subclass we call **match/match part** data. This consists of top level ``match`` features, with a child ``match_part`` |
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| diff -r 6b774e9d6387 -r 0ae74c70b267 macros.xml --- a/macros.xml Tue Jul 16 05:08:10 2019 -0400 +++ b/macros.xml Fri Aug 30 03:36:39 2019 -0400 |
| [ |
| @@ -14,11 +14,11 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">galaxy3</token> + <token name="@WRAPPER_VERSION@">galaxy4</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** -This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche +This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC ]]> </token> |