| Previous changeset 24:fa30df9b79c2 (2019-01-16) Next changeset 26:08776ba76cf5 (2019-02-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f |
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modified:
jbrowse-fromdir.xml jbrowse.py jbrowse.xml macros.xml readme.rst test-data/bam/test.xml test-data/gencode/test-1.xml test-data/gencode/test-data_table.xml test-data/gencode/test.xml test-data/gff3/test.xml test-data/menus/test.xml test-data/track_config/test.xml |
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added:
test-data/endpoints/test.xml |
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| diff -r fa30df9b79c2 -r 1cfc579079a6 jbrowse-fromdir.xml --- a/jbrowse-fromdir.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/jbrowse-fromdir.xml Tue Jan 29 05:34:16 2019 -0500 |
| [ |
| @@ -4,8 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ ## Create output directory mkdir -p $output.files_path && ## Copy in jbrowse |
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| diff -r fa30df9b79c2 -r 1cfc579079a6 jbrowse.py --- a/jbrowse.py Wed Jan 16 03:28:29 2019 -0500 +++ b/jbrowse.py Tue Jan 29 05:34:16 2019 -0500 |
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| b'@@ -263,6 +263,9 @@\n \n \n def etree_to_dict(t):\n+ if t is None:\n+ return {}\n+\n d = {t.tag: {} if t.attrib else None}\n children = list(t)\n if children:\n@@ -381,15 +384,40 @@\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+ p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n+ output, err = p.communicate()\n+ retcode = p.returncode\n+ if retcode != 0:\n+ log.error(\'cd %s && %s\', self.outdir, command)\n+ log.error(output)\n+ log.error(err)\n+ raise RuntimeError("Command failed with exit code %s" % (retcode))\n+\n def _jbrowse_bin(self, command):\n return os.path.realpath(os.path.join(self.jbrowse, \'bin\', command))\n \n def process_genomes(self):\n for genome_node in self.genome_paths:\n- # TODO: Waiting on https://github.com/GMOD/jbrowse/pull/884\n+ # We only expect one input genome per run. This for loop is just\n+ # easier to write than the alternative / catches any possible\n+ # issues.\n+\n+ # Copy the file in workdir, prepare-refseqs.pl will copy it to jbrowse\'s data dir\n+ local_genome = os.path.realpath(\'./genome.fasta\')\n+ shutil.copy(genome_node[\'path\'], local_genome)\n+\n+ cmd = [\'samtools\', \'faidx\', local_genome]\n+ self.subprocess_check_call(cmd)\n+\n self.subprocess_check_call([\n \'perl\', self._jbrowse_bin(\'prepare-refseqs.pl\'),\n- \'--fasta\', genome_node[\'path\']])\n+ \'--trackConfig\', json.dumps({\'metadata\': genome_node[\'meta\']}),\n+ \'--indexed_fasta\', os.path.realpath(local_genome)])\n+\n+ os.unlink(local_genome)\n+ os.unlink(local_genome + \'.fai\')\n \n def generate_names(self):\n # Generate names\n@@ -420,7 +448,7 @@\n return\n \n tmp = tempfile.NamedTemporaryFile(delete=False)\n- tmp.write(json.dumps(json_data))\n+ json.dump(json_data, tmp)\n tmp.close()\n cmd = [\'perl\', self._jbrowse_bin(\'add-track-json.pl\'), tmp.name,\n os.path.join(\'data\', \'trackList.json\')]\n@@ -430,7 +458,7 @@\n def _blastxml_to_gff3(self, xml, min_gap=10):\n gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)\n cmd = [\'python\', os.path.join(INSTALLED_TO, \'blastxml_to_gapped_gff3.py\'),\n- \'--trim\', \'--trim_end\', \'--min_gap\', str(min_gap), xml]\n+ \'--trim\', \'--trim_end\', \'--include_seq\', \'--min_gap\', str(min_gap), xml]\n log.debug(\'cd %s && %s > %s\', self.outdir, \' \'.join(cmd), gff3_unrebased.name)\n subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)\n gff3_unrebased.close()\n@@ -453,27 +481,23 @@\n shutil.copy(gff3_rebased.name, gff3)\n os.unlink(gff3_rebased.name)\n \n- config = {\n- \'glyph\': \'JBrowse/View/FeatureGlyph/Segments\',\n- "category": trackData[\'category\'],\n- }\n+ dest = os.path.join(self.outdir, \'data\', \'raw\', trackData[\'label\'] + \'.gff\')\n \n- clientConfig = trackData[\'style\']\n+ self._sort_gff(gff3, dest)\n \n- cmd = [\'perl\', self._jbrowse_bin(\'flatfile-to-json.pl\'),\n- \'--gff\', gff3,\n- \'--trackLabel\', trackData[\'label\'],\n- \'--key\', trackData[\'key\'],\n- \'--clientConfig\', json.dumps(clientConfig),\n- \'--config\', json.dumps(config),\n- \'--trackType\', \'BlastView/View/Track/CanvasFeatures\'\n- ]\n+ url = os.path.join(\'raw\', trackData[\'label\'] + \'.gff.gz\')\n+ trackData.update({\n+ "urlTemplate": url,\n+ "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",\n+ })\n \n- # class'..b"cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57',\n- 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',\n- 'name': 'ComboTrackSelector'\n- })\n+ # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere\n+ # extra_data['plugins'].append({\n+ # 'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57/',\n+ # 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',\n+ # 'name': 'ComboTrackSelector'\n+ # })\n \n if plugins['theme'] == 'Minimalist':\n extra_data['plugins'].append({\n@@ -911,25 +1022,57 @@\n 'name': 'DarkTheme'\n })\n \n- GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text\n- # Sometimes this comes as `localhost` without a protocol\n- if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):\n- # so we'll prepend `http://` and hope for the best. Requests *should*\n- # be GET and not POST so it should redirect OK\n- GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL\n+ if plugins['BlastView'] == 'True':\n+ extra_data['plugins_python'].append('BlastView')\n+ extra_data['plugins'].append({\n+ 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/',\n+ 'name': 'BlastView'\n+ })\n \n for track in root.findall('tracks/track'):\n track_conf = {}\n track_conf['trackfiles'] = []\n \n- for x in track.findall('files/trackFile'):\n+ is_multi_bigwig = False\n+ try:\n+ if track.find('options/wiggle/multibigwig') and (track.find('options/wiggle/multibigwig').text == 'True'):\n+ is_multi_bigwig = True\n+ multi_bigwig_paths = []\n+ except KeyError:\n+ pass\n+\n+ trackfiles = track.findall('files/trackFile')\n+ if trackfiles:\n+ for x in track.findall('files/trackFile'):\n+ if is_multi_bigwig:\n+ multi_bigwig_paths.append((x.attrib['label'], os.path.realpath(x.attrib['path'])))\n+ else:\n+ if trackfiles:\n+ metadata = metadata_from_node(x.find('metadata'))\n+\n+ track_conf['trackfiles'].append((\n+ os.path.realpath(x.attrib['path']),\n+ x.attrib['ext'],\n+ x.attrib['label'],\n+ metadata\n+ ))\n+ else:\n+ # For tracks without files (rest, sparql)\n+ track_conf['trackfiles'].append((\n+ '', # N/A, no path for rest or sparql\n+ track.attrib['format'],\n+ track.find('options/label').text,\n+ {}\n+ ))\n+\n+ if is_multi_bigwig:\n metadata = metadata_from_node(x.find('metadata'))\n \n track_conf['trackfiles'].append((\n- os.path.realpath(x.attrib['path']),\n- x.attrib['ext'],\n- x.attrib['label'],\n- metadata\n+ multi_bigwig_paths, # Passing an array of paths to represent as one track\n+ 'bigwig_multiple',\n+ 'MultiBigWig', # Giving an hardcoded name for now\n+ {} # No metadata for multiple bigwig\n ))\n \n track_conf['category'] = track.attrib['cat']\n@@ -937,7 +1080,7 @@\n try:\n # Only pertains to gff3 + blastxml. TODO?\n track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}\n- except TypeError as te:\n+ except TypeError:\n track_conf['style'] = {}\n pass\n track_conf['conf'] = etree_to_dict(track.find('options'))\n" |
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| diff -r fa30df9b79c2 -r 1cfc579079a6 jbrowse.xml --- a/jbrowse.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/jbrowse.xml Tue Jan 29 05:34:16 2019 -0500 |
| [ |
| b'@@ -4,9 +4,8 @@\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n- <expand macro="stdio"/>\n <version_command>python \'${__tool_directory__}/jbrowse.py\' --version</version_command>\n- <command><![CDATA[\n+ <command detect_errors="aggressive"><![CDATA[\n #if $action.action_select == "create":\n mkdir -p $output.files_path &&\n #else:\n@@ -73,31 +72,29 @@\n <metadata />\n </genome>s\n #else\n- #for $genome in $reference_genome.genomes:\n- <genome path="$genome">\n- <metadata>\n- <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"\n- size="${genome.get_size(nice_size=True)}"\n- edam_format="${genome.datatype.edam_format}"\n- file_ext="${genome.ext}" />\n- <history id="${__app__.security.encode_id($genome.history_id)}"\n- user_email="${genome.history.user.email}"\n- user_id="${genome.history.user_id}"\n- display_name="${genome.history.get_display_name()}"/>\n- <metadata\n- #for (key, value) in $genome.get_metadata().items():\n- #if "_types" not in $key:\n- ${key}="${value}"\n- #end if\n- #end for\n- />\n- <tool\n- tool_id="${genome.creating_job.tool_id}"\n- tool_version="${genome.creating_job.tool_version}"\n- />\n- </metadata>\n- </genome>\n- #end for\n+ <genome path="$reference_genome.genome">\n+ <metadata>\n+ <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"\n+ size="${reference_genome.genome.get_size(nice_size=True)}"\n+ edam_format="${reference_genome.genome.datatype.edam_format}"\n+ file_ext="${reference_genome.genome.ext}" />\n+ <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"\n+ user_email="${reference_genome.genome.history.user.email}"\n+ user_id="${reference_genome.genome.history.user_id}"\n+ display_name="${reference_genome.genome.history.get_display_name()}"/>\n+ <metadata\n+ #for (key, value) in $reference_genome.genome.get_metadata().items():\n+ #if "_types" not in $key:\n+ ${key}="${value}"\n+ #end if\n+ #end for\n+ />\n+ <tool\n+ tool_id="${reference_genome.genome.creating_job.tool_id}"\n+ tool_version="${reference_genome.genome.creating_job.tool_version}"\n+ />\n+ </metadata>\n+ </genome>\n #end if\n </genomes>\n <general>\n@@ -117,12 +114,8 @@\n <tracks>\n #for $tg in $track_groups:\n #for $track in $tg.data_tracks:\n- #if $track.data_format.data_format_select == "rest":\n <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n- <url>${track.data_format.url}</url>\n- </track>\n- #else:\n- <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n+ #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql":\n <files>\n #for $dataset in $track.data_format.annotation:\n <trackFile pa'..b' <param name="category" value="External endpoints" />\n+ <repeat name="data_tracks">\n+ <conditional name="data_format">\n+ <param name="data_format_select" value="rest"/>\n+ <param name="url" value="http://example.org.external/rest_api/"/>\n+ <param name="label" value="Rest api"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="data_tracks">\n+ <conditional name="data_format">\n+ <param name="data_format_select" value="sparql"/>\n+ <param name="url" value="http://example.org.external/sparql/"/>\n+ <param name="label" value="Sparql endpoint"/>\n+ <param name="query" value=" DEFINE sql:select-option \'order\'\n+ prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n+ select ?start,\n+ ?end,\n+ IF( ?faldo_type = faldo:ForwardStrandPosition,\n+ 1,\n+ IF( ?faldo_type = faldo:ReverseStrandPosition,\n+ -1,\n+ 0\n+ )\n+ ) as ?strand,\n+ str(?obj_type_name) as ?type,\n+ str(?label) as ?name,\n+ str(?obj_name) as ?description,\n+ ?obj as ?uniqueID,\n+ ?parent as ?parentUniqueID\n+ where {\n+ values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }\n+ }"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+\n+ <param name="uglyTestingHack" value="enabled" />\n+ <output name="output" file="endpoints/test.xml" lines_diff="48"/>\n+ </test>\n </tests>\n <help><![CDATA[\n JBrowse-in-Galaxy\n@@ -952,9 +1062,9 @@\n javascript functions to handle colouring of features which would be\n nearly impossible to write without the assistance of this tool.\n \n-The JBrowse-in-Galaxy tool is maintained by `Eric\n-Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you\n-encounter missing features or bugs.\n+The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC\n+<https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you\n+with missing features or bugs in the tool.\n \n Options\n -------\n@@ -966,11 +1076,12 @@\n will be shown from the dropdown selector within JBrowse, this is a known\n issue.\n \n-**Standalone Instances** are a somewhat in-development feature.\n+**Standalone Instances** enable you to have either a complete JBrowse instance\n+in a dataset, or just the data directory without JBrowse (e.g. for Apollo).\n Currently Galaxy copies the entire JBrowse directory in order to have a\n complete, downloadable file that contains a ready-to-go JBrowse\n instance. This is obviously an anti-feature because users don\'t want a\n-complete copy of JBrowse (6-20Mb) that\'s duplicated for every JBrowse\n+complete copy of JBrowse (12Mb) that\'s duplicated for every JBrowse\n dataset in their history, and admins don\'t want useless copies of\n JBrowse on disk. Unfortunately we have not come up with the perfect\n solution just yet, but we\'re working on it! In the meantime, users have\n@@ -981,10 +1092,7 @@\n \n **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,\n which allows users to specify a non standard genetic code, and have\n-JBrowse highlight the correct start and stop codons. If you would like\n-to use a coding table not provided by this list, please let\n-`me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for\n-this.\n+JBrowse highlight the correct start and stop codons.\n \n **Track Groups** represent a set of tracks in a single category. These\n can be used to let your users understand relationships between large\n@@ -1086,8 +1194,7 @@\n \n This is *strongly discouraged* for high coverage density datasets.\n Unfortunately there are no other configuration options exposed for bam\n-files. If you find JBrowse options you wish to see exposed, please let\n-`me <mailto:esr+jig@tamu.edu>`__ know.\n+files.\n \n BlastXML\n ~~~~~~~~\n' |
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| diff -r fa30df9b79c2 -r 1cfc579079a6 macros.xml --- a/macros.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/macros.xml Tue Jan 29 05:34:16 2019 -0500 |
| [ |
| @@ -1,27 +1,20 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.12.5</token> + <token name="@TOOL_VERSION@">1.16.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement> <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.66">biopython</requirement> - <requirement type="package" version="0.6.2">bcbiogff</requirement> - <requirement type="package" version="1.2">samtools</requirement> - <requirement type="package" version="3.11">pyyaml</requirement> + <requirement type="package" version="1.72">biopython</requirement> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="3.13">pyyaml</requirement> + <requirement type="package" version="0.2.6">tabix</requirement> <yield/> </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">galaxy3</token> - <xml name="stdio"> - <stdio> - <exit_code range="1:"/> - <exit_code range=":-1"/> - <regex match="Error:"/> - <regex match="Exception:"/> - </stdio> - </xml> + <token name="@WRAPPER_VERSION@">galaxy0</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** |
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| diff -r fa30df9b79c2 -r 1cfc579079a6 readme.rst --- a/readme.rst Wed Jan 16 03:28:29 2019 -0500 +++ b/readme.rst Tue Jan 29 05:34:16 2019 -0500 |
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| @@ -25,18 +25,31 @@ History ======= -- 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector), - track metadata -- 0.5.2 Support for CanvasFeatures options. -- 0.5.1 Support for contextual menus. Conda tests. -- 0.5 Update existing instances on disk. Index names. Support HTML tracks - instead of Canvas. Support default tracks. General JBrowse optinos -- 0.4 Support for dataset collections and customisation of tracks including - labelling, colours, styling. Added support for genetic code selection. - Fixed package installation recipe issues. -- 0.3 Added support for BigWig, etc. -- 0.2 Added support for BAM, Blast, VCF. -- 0.1 Initial public release. +- 1.16.1+galaxy0 + + - UPDATED to JBrowse 1.16.1 + - ADDED support for MultiBigWig plugin + - ADDED support for tabix indexing of fasta and gff + - ADDED support for REST and SPARQL endpoints + - ADDED option to change chunk size for BAM tracks + - FIXED loading of VCF files. They were gzipped and the URLs were incorrect + - FIXED metadata on tracks types other than GFF+HTML + - FIXED infrastructure URL parsing (and embedding in links) for some tracks + - REMOVED support for selecting multiple genomes as input due to tracking of track metadata + - REMOVED support for themes as JBrowse no longer allow runtime loading of plugins + +- 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector), + track metadata +- 0.5.2 Support for CanvasFeatures options. +- 0.5.1 Support for contextual menus. Conda tests. +- 0.5 Update existing instances on disk. Index names. Support HTML tracks + instead of Canvas. Support default tracks. General JBrowse optinos +- 0.4 Support for dataset collections and customisation of tracks including + labelling, colours, styling. Added support for genetic code selection. + Fixed package installation recipe issues. +- 0.3 Added support for BigWig, etc. +- 0.2 Added support for BAM, Blast, VCF. +- 0.1 Initial public release. Wrapper License (MIT/BSD Style) =============================== |
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| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/bam/test.xml --- a/test-data/bam/test.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/bam/test.xml Tue Jan 29 05:34:16 2019 -0500 |
| [ |
| b'@@ -3,27 +3,27 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome path="/tmp/tmpfqQZDj/files/000/dataset_2.dat">\n- <metadata>\n- <dataset id="9a22496ee796fbfc" hid="1"\n- size="171.6 KB"\n- edam_format="format_1929"\n- file_ext="fasta" />\n- <history id="fa6d20d0fb68383f"\n- user_email="test@bx.psu.edu"\n- user_id="2"\n- display_name="test_history"/>\n- <metadata\n- dbkey="hg17"\n- data_lines="2881"\n- sequences="1"\n- />\n- <tool\n- tool_id="upload1"\n- tool_version="1.1.4"\n- />\n- </metadata>\n- </genome>\n+ <genome path="/tmp/tmpWtvfKr/files/000/dataset_20.dat">\n+ <metadata>\n+ <dataset id="b28067233c6d9fa0" hid="1"\n+ size="171.6 KB"\n+ edam_format="format_1929"\n+ file_ext="fasta" />\n+ <history id="fa6d20d0fb68383f"\n+ user_email="test@bx.psu.edu"\n+ user_id="2"\n+ display_name="test_history"/>\n+ <metadata\n+ dbkey="?"\n+ data_lines="2881"\n+ sequences="1"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.6"\n+ />\n+ </metadata>\n+ </genome>\n </genomes>\n <general>\n <defaultLocation></defaultLocation>\n@@ -40,33 +40,33 @@\n <galaxyUrl>http://localhost</galaxyUrl>\n </metadata>\n <tracks>\n- <track cat="Aligned reads" format="pileup" visibility="default_off">\n+ <track cat="Auto Coloured" format="pileup" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpfqQZDj/files/000/dataset_1.dat" ext="bam" label="merlin-sample.bam">\n+ <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_21.dat" ext="bam" label="merlin-sample.bam">\n <metadata>\n- <dataset id="2891970512fa2d5a" hid="1"\n+ <dataset id="c18708cec3343c17" hid="2"\n size="12.9 KB"\n edam_format="format_2572"\n file_ext="bam" />\n- <history id="2891970512fa2d5a"\n- user_email="planemo@galaxyproject.org"\n- user_id="1"\n- display_name="Unnamed history"/>\n+ <history id="fa6d20d0fb68383f"\n+ user_email="test@bx.psu.edu"\n+ user_id="2"\n+ display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n- bam_index="__lt__galaxy.model.MetadataFile object at 0x7fc42c1d18d0__gt__"\n+ dbkey="?"\n+ bam_index="__lt__galaxy.model.MetadataFile object at 0x7f6200f6d1d0__gt__"\n bam_version="1.3"\n sort_order="coordinate"\n read_groups=""\n- reference_names="[SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc4484b3170 on: u_'..b'_sq__ellipsis__sq____gt__) object at 7f6200e95788 on: __sq__MAPQ__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95730 on: __sq__CIGAR__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95d60 on: __sq__MRNM__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95d08 on: __sq__MPOS__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95c58 on: __sq__ISIZE__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e952b8 on: __sq__SEQ__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95418 on: __sq__QUAL__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f6200e95998 on: __sq__OPT__sq__]"\n />\n <tool\n tool_id="upload1"\n- tool_version="1.1.4"\n+ tool_version="1.1.6"\n />\n </metadata>\n </trackFile>\n@@ -77,7 +77,7 @@\n <pileup>\n <auto_snp>false</auto_snp>\n <bam_indices>\n- <bam_index>/tmp/tmpfqQZDj/files/_metadata_files/000/metadata_1.dat</bam_index>\n+ <bam_index>/tmp/tmpWtvfKr/files/_metadata_files/000/metadata_1.dat</bam_index>\n </bam_indices>\n </pileup>\n </options>\n' |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/endpoints/test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/endpoints/test.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| @@ -0,0 +1,106 @@ +<?xml version="1.0"?> +<root> + <metadata> + <gencode>11</gencode> + <genomes> + <genome path="/tmp/tmpdcb31B/files/000/dataset_24.dat"> + <metadata> + <dataset id="a1e670e1ea0da54b" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="a90a30fafe298e1e" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </genome> + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>20</trackPadding> + + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>true</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + <galaxyUrl>http://localhost</galaxyUrl> + </metadata> + <tracks> + <track cat="External endpoints" format="rest" visibility="default_off"> + + <options> + <style> + <overridePlugins>False</overridePlugins> + <overrideDraggable>False</overrideDraggable> + <className>feature</className> + <description>Hit_titles</description> + <label>description</label> + <height>600px</height> + <maxHeight>600</maxHeight> + </style> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + <menus> + </menus> + + <label>Rest api</label> + <rest> + <url>http://example.org.external/rest_api/</url> + </rest> + </options> + </track> + <track cat="External endpoints" format="sparql" visibility="default_off"> + + <options> + <style> + <overridePlugins>False</overridePlugins> + <overrideDraggable>False</overrideDraggable> + <className>feature</className> + <description>Hit_titles</description> + <label>description</label> + <height>600px</height> + <maxHeight>600</maxHeight> + </style> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + <menus> + </menus> + + <label>Sparql endpoint</label> + <sparql> + <url>http://example.org.external/sparql/</url> + <query> DEFINE sql:select-option 'order' prefix rdf: __lt__http://www.w3.org/1999/02/22-rdf-syntax-ns#__gt__ select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }</query> + </sparql> + </options> + </track> + </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + BlastView="True" + theme="" + /> +</root> |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/gencode/test-1.xml --- a/test-data/gencode/test-1.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/gencode/test-1.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| @@ -3,27 +3,27 @@ <metadata> <gencode>1</gencode> <genomes> - <genome path="/tmp/tmpnh6QWY/files/000/dataset_1.dat"> - <metadata> - <dataset id="2891970512fa2d5a" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="2891970512fa2d5a" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="hg17" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.4" - /> - </metadata> - </genome> + <genome path="/tmp/tmpZA6JJa/files/000/dataset_1.dat"> + <metadata> + <dataset id="2891970512fa2d5a" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="2891970512fa2d5a" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </genome> </genomes> <general> <defaultLocation></defaultLocation> @@ -37,7 +37,7 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> - <galaxyUrl>http://localhost:8080</galaxyUrl> + <galaxyUrl>http://localhost</galaxyUrl> </metadata> <tracks> </tracks> @@ -45,6 +45,7 @@ ComboTrackSelector="" Bookmarks="" GCContent="" + BlastView="True" theme="" /> </root> |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/gencode/test-data_table.xml --- a/test-data/gencode/test-data_table.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/gencode/test-data_table.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| @@ -27,6 +27,7 @@ ComboTrackSelector="" Bookmarks="" GCContent="" + BlastView="True" theme="" /> </root> |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/gencode/test.xml --- a/test-data/gencode/test.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/gencode/test.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| @@ -3,27 +3,27 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpnh6QWY/files/000/dataset_3.dat"> - <metadata> - <dataset id="54f2a3a23292eb07" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="5729865256bc2525" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="hg17" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.4" - /> - </metadata> - </genome> + <genome path="/tmp/tmpZA6JJa/files/000/dataset_3.dat"> + <metadata> + <dataset id="54f2a3a23292eb07" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="5729865256bc2525" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </genome> </genomes> <general> <defaultLocation></defaultLocation> @@ -37,7 +37,7 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> - <galaxyUrl>http://localhost:8080</galaxyUrl> + <galaxyUrl>http://localhost</galaxyUrl> </metadata> <tracks> </tracks> |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/gff3/test.xml --- a/test-data/gff3/test.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/gff3/test.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| b'@@ -3,27 +3,27 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome path="/tmp/tmpnh6QWY/files/000/dataset_5.dat">\n- <metadata>\n- <dataset id="7b55dbb89df8f4e5" hid="1"\n- size="171.6 KB"\n- edam_format="format_1929"\n- file_ext="fasta" />\n- <history id="54f2a3a23292eb07"\n- user_email="test@bx.psu.edu"\n- user_id="2"\n- display_name="test_history"/>\n- <metadata\n- dbkey="hg17"\n- data_lines="2881"\n- sequences="1"\n- />\n- <tool\n- tool_id="upload1"\n- tool_version="1.1.4"\n- />\n- </metadata>\n- </genome>\n+ <genome path="/tmp/tmpWtvfKr/files/000/dataset_5.dat">\n+ <metadata>\n+ <dataset id="7b55dbb89df8f4e5" hid="1"\n+ size="171.6 KB"\n+ edam_format="format_1929"\n+ file_ext="fasta" />\n+ <history id="54f2a3a23292eb07"\n+ user_email="test@bx.psu.edu"\n+ user_id="2"\n+ display_name="test_history"/>\n+ <metadata\n+ dbkey="?"\n+ data_lines="2881"\n+ sequences="1"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.6"\n+ />\n+ </metadata>\n+ </genome>\n </genomes>\n <general>\n <defaultLocation></defaultLocation>\n@@ -37,12 +37,12 @@\n <show_menu>true</show_menu>\n <hideGenomeOptions>false</hideGenomeOptions>\n </general>\n- <galaxyUrl>http://localhost:8080</galaxyUrl>\n+ <galaxyUrl>http://localhost</galaxyUrl>\n </metadata>\n <tracks>\n <track cat="Auto Coloured" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">\n+ <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_6.dat" ext="gff3" label="A.gff">\n <metadata>\n <dataset id="fa6d20d0fb68383f" hid="2"\n size="2.3 KB"\n@@ -53,7 +53,7 @@\n user_id="2"\n display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n+ dbkey="?"\n data_lines="27"\n comment_lines="19"\n columns="9"\n@@ -63,11 +63,11 @@\n />\n <tool\n tool_id="upload1"\n- tool_version="1.1.4"\n+ tool_version="1.1.6"\n />\n </metadata>\n </trackFile>\n- <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">\n+ <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_7.dat" ext="gff3" label="B.gff">\n <metadata>\n <dataset id="683bc220e21425bb" hid="3"\n size="2.3 KB"\n@@ -78,7 +78,7 @@\n user_id="2"\n display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n+ dbkey="?"\n data_lines="27"\n comment_lines="19"\n columns="9"\n@@ -88,11 +88,11 @@\n />\n <tool\n tool_id="upload1"\n- to'..b' size="2.3 KB"\n@@ -356,7 +356,7 @@\n user_id="2"\n display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n+ dbkey="?"\n data_lines="27"\n comment_lines="19"\n columns="9"\n@@ -366,7 +366,7 @@\n />\n <tool\n tool_id="upload1"\n- tool_version="1.1.4"\n+ tool_version="1.1.6"\n />\n </metadata>\n </trackFile>\n@@ -407,7 +407,7 @@\n </track>\n <track cat="Scaled Colour" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">\n+ <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">\n <metadata>\n <dataset id="5449172d6ff5669b" hid="6"\n size="2.3 KB"\n@@ -418,7 +418,7 @@\n user_id="2"\n display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n+ dbkey="?"\n data_lines="27"\n comment_lines="19"\n columns="9"\n@@ -428,7 +428,7 @@\n />\n <tool\n tool_id="upload1"\n- tool_version="1.1.4"\n+ tool_version="1.1.6"\n />\n </metadata>\n </trackFile>\n@@ -469,7 +469,7 @@\n </track>\n <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">\n+ <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">\n <metadata>\n <dataset id="9ce08b2254e4d5ed" hid="7"\n size="103.3 KB"\n@@ -480,7 +480,7 @@\n user_id="2"\n display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n+ dbkey="?"\n data_lines="556"\n comment_lines="2"\n columns="9"\n@@ -490,7 +490,7 @@\n />\n <tool\n tool_id="upload1"\n- tool_version="1.1.4"\n+ tool_version="1.1.6"\n />\n </metadata>\n </trackFile>\n@@ -523,7 +523,7 @@\n </track>\n <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">\n+ <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_12.dat" ext="gff3" label="2.gff">\n <metadata>\n <dataset id="80b8022ff3f677b7" hid="8"\n size="326 bytes"\n@@ -534,7 +534,7 @@\n user_id="2"\n display_name="test_history"/>\n <metadata\n- dbkey="hg17"\n+ dbkey="?"\n data_lines="3"\n comment_lines="3"\n columns="9"\n@@ -544,7 +544,7 @@\n />\n <tool\n tool_id="upload1"\n- tool_version="1.1.4"\n+ tool_version="1.1.6"\n />\n </metadata>\n </trackFile>\n@@ -581,6 +581,7 @@\n ComboTrackSelector=""\n Bookmarks=""\n GCContent=""\n+ BlastView="True"\n theme=""\n />\n </root>\n' |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/menus/test.xml --- a/test-data/menus/test.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/menus/test.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| @@ -3,27 +3,27 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpnh6QWY/files/000/dataset_14.dat"> - <metadata> - <dataset id="1ae74d26531588b0" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="hg17" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.4" - /> - </metadata> - </genome> + <genome path="/tmp/tmpWtvfKr/files/000/dataset_14.dat"> + <metadata> + <dataset id="1ae74d26531588b0" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="8155e4b4bf1581ff" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </genome> </genomes> <general> <defaultLocation></defaultLocation> @@ -37,12 +37,12 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> - <galaxyUrl>http://localhost:8080</galaxyUrl> + <galaxyUrl>http://localhost</galaxyUrl> </metadata> <tracks> <track cat="With menu or index" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_15.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_15.dat" ext="gff3" label="1.gff"> <metadata> <dataset id="440a6c2b5d9efe20" hid="2" size="2.3 KB" @@ -53,7 +53,7 @@ user_id="2" display_name="test_history"/> <metadata - dbkey="hg17" + dbkey="?" data_lines="27" comment_lines="19" columns="9" @@ -63,7 +63,7 @@ /> <tool tool_id="upload1" - tool_version="1.1.4" + tool_version="1.1.6" /> </metadata> </trackFile> @@ -110,7 +110,7 @@ </track> <track cat="With menu or index" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_15.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_15.dat" ext="gff3" label="1.gff"> <metadata> <dataset id="440a6c2b5d9efe20" hid="2" size="2.3 KB" @@ -121,7 +121,7 @@ user_id="2" display_name="test_history"/> <metadata - dbkey="hg17" + dbkey="?" data_lines="27" comment_lines="19" columns="9" @@ -131,7 +131,7 @@ /> <tool tool_id="upload1" - tool_version="1.1.4" + tool_version="1.1.6" /> </metadata> </trackFile> @@ -169,4 +169,4 @@ GCContent="" theme="" /> -</root> +</root> \ No newline at end of file |
| b |
| diff -r fa30df9b79c2 -r 1cfc579079a6 test-data/track_config/test.xml --- a/test-data/track_config/test.xml Wed Jan 16 03:28:29 2019 -0500 +++ b/test-data/track_config/test.xml Tue Jan 29 05:34:16 2019 -0500 |
| b |
| @@ -3,27 +3,27 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpnh6QWY/files/000/dataset_17.dat"> - <metadata> - <dataset id="27ee89e2e3d631e0" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="7b55dbb89df8f4e5" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="hg17" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.4" - /> - </metadata> - </genome> + <genome path="/tmp/tmpWtvfKr/files/000/dataset_17.dat"> + <metadata> + <dataset id="27ee89e2e3d631e0" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="7b55dbb89df8f4e5" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </genome> </genomes> <general> <defaultLocation></defaultLocation> @@ -37,12 +37,12 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> - <galaxyUrl>http://localhost:8080</galaxyUrl> + <galaxyUrl>http://localhost</galaxyUrl> </metadata> <tracks> <track cat="With canvas config" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_18.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_18.dat" ext="gff3" label="1.gff"> <metadata> <dataset id="61f03d5eef6f1538" hid="2" size="2.3 KB" @@ -53,7 +53,7 @@ user_id="2" display_name="test_history"/> <metadata - dbkey="hg17" + dbkey="?" data_lines="27" comment_lines="19" columns="9" @@ -63,7 +63,7 @@ /> <tool tool_id="upload1" - tool_version="1.1.4" + tool_version="1.1.6" /> </metadata> </trackFile> @@ -101,4 +101,4 @@ GCContent="" theme="" /> -</root> +</root> \ No newline at end of file |