| Previous changeset 16:b5c5470d7c09 (2017-09-13) Next changeset 18:836d1aa3e89a (2017-11-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 |
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modified:
blastxml_to_gapped_gff3.py gff3_rebase.py jbrowse.py jbrowse.xml macros.xml test-data/bam/test.xml test-data/blastxml/test.xml test-data/bw/data.bw test-data/bw/test.xml test-data/gencode/test-1.xml test-data/gencode/test.xml test-data/gff3/test.xml test-data/menus/test.xml test-data/track_config/test.xml test-data/vcf/test.xml |
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added:
all_fasta.loc.sample |
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| diff -r b5c5470d7c09 -r ff11d442feed all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Wed Nov 15 15:15:27 2017 -0500 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
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| diff -r b5c5470d7c09 -r ff11d442feed blastxml_to_gapped_gff3.py --- a/blastxml_to_gapped_gff3.py Wed Sep 13 13:07:20 2017 -0400 +++ b/blastxml_to_gapped_gff3.py Wed Nov 15 15:15:27 2017 -0500 |
| [ |
| @@ -6,47 +6,58 @@ import sys from BCBio import GFF - logging.basicConfig(level=logging.INFO) log = logging.getLogger(name='blastxml2gff3') -__author__ = "Eric Rasche" -__version__ = "0.4.0" -__maintainer__ = "Eric Rasche" -__email__ = "esr@tamu.edu" - __doc__ = """ BlastXML files, when transformed to GFF3, do not normally show gaps in the blast hits. This tool aims to fill that "gap". """ -def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False): +def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False, include_seq=False): from Bio.Blast import NCBIXML from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.SeqFeature import SeqFeature, FeatureLocation blast_records = NCBIXML.parse(blastxml) - records = [] - for record in blast_records: + for idx_record, record in enumerate(blast_records): # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343 match_type = { # Currently we can only handle BLASTN, BLASTP 'BLASTN': 'nucleotide_match', 'BLASTP': 'protein_match', }.get(record.application, 'match') - rec = SeqRecord(Seq("ACTG"), id=record.query) - for hit in record.alignments: - for hsp in hit.hsps: + recid = record.query + if ' ' in recid: + recid = recid[0:recid.index(' ')] + + rec = SeqRecord(Seq("ACTG"), id=recid) + for idx_hit, hit in enumerate(record.alignments): + for idx_hsp, hsp in enumerate(hit.hsps): qualifiers = { + "ID": 'b2g.%s.%s.%s' % (idx_record, idx_hit, idx_hsp), "source": "blast", "score": hsp.expect, "accession": hit.accession, "hit_id": hit.hit_id, "length": hit.length, - "hit_titles": hit.title.split(' >') + "hit_titles": hit.title.split(' >'), } + if include_seq: + qualifiers.update({ + 'blast_qseq': hsp.query, + 'blast_sseq': hsp.sbjct, + 'blast_mseq': hsp.match, + }) + + for prop in ('score', 'bits', 'identities', 'positives', + 'gaps', 'align_length', 'strand', 'frame', + 'query_start', 'query_end', 'sbjct_start', + 'sbjct_end'): + qualifiers['blast_' + prop] = getattr(hsp, prop, None) + desc = hit.title.split(' >')[0] qualifiers['description'] = desc[desc.index(' '):] @@ -62,14 +73,11 @@ # protein. parent_match_end = hsp.query_start + hit.length + hsp.query.count('-') - # However, if the user requests that we trim the feature, then - # we need to cut the ``match`` start to 0 to match the parent feature. - # We'll also need to cut the end to match the query's end. It (maybe) - # should be the feature end? But we don't have access to that data, so - # We settle for this. + # If we trim the left end, we need to trim without losing information. + used_parent_match_start = parent_match_start if trim: if parent_match_start < 1: - parent_match_start = 0 + used_parent_match_start = 0 if trim or trim_end: if parent_match_end > hsp.query_end: @@ -77,7 +85,7 @@ # The ``match`` feature will hold one or more ``match_part``s top_feature = SeqFeature( - FeatureLocation(parent_match_start, parent_match_end), + FeatureLocation(used_parent_match_start, parent_match_end), type=match_type, strand=0, qualifiers=qualifiers ) @@ -87,19 +95,15 @@ "source": "blast", } top_feature.sub_features = [] - for start, end, cigar in generate_parts(hsp.query, hsp.match, - hsp.sbjct, - ignore_under=min_gap): + for idx_part, (start, end, cigar) in \ + enumerate(generate_parts(hsp.query, hsp.match, + hsp.sbjct, + ignore_under=min_gap)): part_qualifiers['Gap'] = cigar - part_qualifiers['ID'] = hit.hit_id + part_qualifiers['ID'] = qualifiers['ID'] + ('.%s' % idx_part) - if trim: - # If trimming, then we start relative to the - # match's start - match_part_start = parent_match_start + start - else: - # Otherwise, we have to account for the subject start's location - match_part_start = parent_match_start + hsp.sbjct_start + start - 1 + # Otherwise, we have to account for the subject start's location + match_part_start = parent_match_start + hsp.sbjct_start + start - 1 # We used to use hsp.align_length here, but that includes # gaps in the parent sequence @@ -117,8 +121,7 @@ rec.features.append(top_feature) rec.annotations = {} - records.append(rec) - return records + yield rec def __remove_query_gaps(query, match, subject): @@ -253,11 +256,13 @@ if __name__ == '__main__': parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='') - parser.add_argument('blastxml', type=open, help='Blast XML Output') + parser.add_argument('blastxml', type=argparse.FileType("r"), help='Blast XML Output') parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3) parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature') parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene') + parser.add_argument('--include_seq', action='store_true', help='Include sequence') args = parser.parse_args() - result = blastxml2gff3(**vars(args)) - GFF.write(result, sys.stdout) + for rec in blastxml2gff3(**vars(args)): + if len(rec.features): + GFF.write([rec], sys.stdout) |
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| diff -r b5c5470d7c09 -r ff11d442feed gff3_rebase.py --- a/gff3_rebase.py Wed Sep 13 13:07:20 2017 -0400 +++ b/gff3_rebase.py Wed Nov 15 15:15:27 2017 -0500 |
| [ |
| @@ -83,18 +83,25 @@ def __get_features(child, interpro=False): child_features = {} for rec in GFF.parse(child): + # Only top level for feature in rec.features: + # Get the record id as parent_feature_id (since this is how it will be during remapping) parent_feature_id = rec.id + # If it's an interpro specific gff3 file if interpro: + # Then we ignore polypeptide features as they're useless if feature.type == 'polypeptide': continue - if '_' in parent_feature_id: - parent_feature_id = parent_feature_id[parent_feature_id.index('_') + 1:] + # If there's an underscore, we strip up to that underscore? + # I do not know the rationale for this, removing. + # if '_' in parent_feature_id: + # parent_feature_id = parent_feature_id[parent_feature_id.index('_') + 1:] try: child_features[parent_feature_id].append(feature) except KeyError: child_features[parent_feature_id] = [feature] + # Keep a list of feature objects keyed by parent record id return child_features @@ -132,23 +139,29 @@ __update_feature_location(subfeature, parent, protein2dna) -def rebase(parent, child, interpro=False, protein2dna=False): +def rebase(parent, child, interpro=False, protein2dna=False, map_by='ID'): + # get all of the features we will be re-mapping in a dictionary, keyed by parent feature ID child_features = __get_features(child, interpro=interpro) for rec in GFF.parse(parent): replacement_features = [] for feature in feature_lambda( rec.features, + # Filter features in the parent genome by those that are + # "interesting", i.e. have results in child_features array. + # Probably an unnecessary optimisation. feature_test_qual_value, { - 'qualifier': 'ID', + 'qualifier': map_by, 'attribute_list': child_features.keys(), }, subfeatures=False): - new_subfeatures = child_features[feature.id] - fixed_subfeatures = [] - for x in new_subfeatures: + # Features which will be re-mapped + to_remap = child_features[feature.id] + # TODO: update starts + fixed_features = [] + for x in to_remap: # Then update the location of the actual feature __update_feature_location(x, feature, protein2dna) @@ -156,11 +169,11 @@ for y in ('status', 'Target'): try: del x.qualifiers[y] - except: + except Exception: pass - fixed_subfeatures.append(x) - replacement_features.extend(fixed_subfeatures) + fixed_features.append(x) + replacement_features.extend(fixed_features) # We do this so we don't include the original set of features that we # were rebasing against in our result. rec.features = replacement_features @@ -176,5 +189,6 @@ help='Interpro specific modifications') parser.add_argument('--protein2dna', action='store_true', help='Map protein translated results to original DNA data') + parser.add_argument('--map_by', help='Map by key', default='ID') args = parser.parse_args() rebase(**vars(args)) |
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| diff -r b5c5470d7c09 -r ff11d442feed jbrowse.py --- a/jbrowse.py Wed Sep 13 13:07:20 2017 -0400 +++ b/jbrowse.py Wed Nov 15 15:15:27 2017 -0500 |
| [ |
| b'@@ -1,7 +1,8 @@\n #!/usr/bin/env python\n import argparse\n-import codecs\n+import binascii\n import copy\n+import datetime\n import hashlib\n import json\n import logging\n@@ -14,9 +15,10 @@\n from collections import defaultdict\n \n from Bio.Data import CodonTable\n-\n logging.basicConfig(level=logging.INFO)\n log = logging.getLogger(\'jbrowse\')\n+TODAY = datetime.datetime.now().strftime("%Y-%m-%d")\n+GALAXY_INFRASTRUCTURE_URL = None\n \n \n class ColorScaling(object):\n@@ -63,6 +65,7 @@\n var color = ({user_spec_color} || search_up(feature, \'color\') || search_down(feature, \'color\') || {auto_gen_color});\n var score = (search_up(feature, \'score\') || search_down(feature, \'score\'));\n {opacity}\n+ if(score === undefined){{ opacity = 1; }}\n var result = /^#?([a-f\\d]{{2}})([a-f\\d]{{2}})([a-f\\d]{{2}})$/i.exec(color);\n var red = parseInt(result[1], 16);\n var green = parseInt(result[2], 16);\n@@ -82,11 +85,11 @@\n """,\n \'blast\': """\n var opacity = 0;\n- if(score == 0.0) {\n+ if(score == 0.0) {{\n opacity = 1;\n- } else{\n+ }} else {{\n opacity = (20 - Math.log10(score)) / 180;\n- }\n+ }}\n """\n }\n \n@@ -128,7 +131,7 @@\n \n def rgb_from_hex(self, hexstr):\n # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back\n- return struct.unpack(\'BBB\', codecs.decode(hexstr, \'hex\'))\n+ return struct.unpack(\'BBB\', binascii.unhexlify(hexstr))\n \n def min_max_gff(self, gff_file):\n min_val = None\n@@ -285,6 +288,44 @@\n INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))\n \n \n+def metadata_from_node(node):\n+ metadata = {}\n+ try:\n+ if len(node.findall(\'dataset\')) != 1:\n+ # exit early\n+ return metadata\n+ except Exception:\n+ return {}\n+\n+ for (key, value) in node.findall(\'dataset\')[0].attrib.items():\n+ metadata[\'dataset_%s\' % key] = value\n+\n+ for (key, value) in node.findall(\'history\')[0].attrib.items():\n+ metadata[\'history_%s\' % key] = value\n+\n+ for (key, value) in node.findall(\'metadata\')[0].attrib.items():\n+ metadata[\'metadata_%s\' % key] = value\n+\n+ for (key, value) in node.findall(\'tool\')[0].attrib.items():\n+ metadata[\'tool_%s\' % key] = value\n+\n+ # Additional Mappings applied:\n+ metadata[\'dataset_edam_format\'] = \'<a target="_blank" href="http://edamontology.org/{0}">{1}</a>\'.format(metadata[\'dataset_edam_format\'], metadata[\'dataset_file_ext\'])\n+ metadata[\'history_user_email\'] = \'<a href="mailto:{0}">{0}</a>\'.format(metadata[\'history_user_email\'])\n+ metadata[\'history_display_name\'] = \'<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>\'.format(\n+ galaxy=GALAXY_INFRASTRUCTURE_URL,\n+ encoded_hist_id=metadata[\'history_id\'],\n+ hist_name=metadata[\'history_display_name\']\n+ )\n+ metadata[\'tool_tool\'] = \'<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>\'.format(\n+ galaxy=GALAXY_INFRASTRUCTURE_URL,\n+ encoded_id=metadata[\'dataset_id\'],\n+ tool_id=metadata[\'tool_tool_id\'],\n+ tool_version=metadata[\'tool_tool_version\'],\n+ )\n+ return metadata\n+\n+\n class JbrowseConnector(object):\n \n def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):\n@@ -312,6 +353,12 @@\n # Ignore if the folder exists\n pass\n \n+ try:\n+ os.makedirs(os.path.join(self.outdir, \'data\', \'raw\'))\n+ except OSError:\n+ # Ignore if the folder exists\n+ pass\n+\n self.process_genomes()\n self.update_gencode()\n \n@@ -338,21 +385,20 @@\n return os.path.realpath(os.path.join(self.jbrowse, \'bin\', command))\n \n def process_genomes(self):\n- for genome_path in self.genome_paths:\n+ for genome_node in self.genome'..b" os.path.realpath(x.attrib['path']),\n+ 'meta': metadata_from_node(x.find('metadata'))\n+ }\n+ for x in root.findall('metadata/genomes/genome')\n+ ],\n standalone=args.standalone,\n gencode=root.find('metadata/gencode').text\n )\n@@ -719,21 +868,74 @@\n 'show_overview': root.find('metadata/general/show_overview').text,\n 'show_menu': root.find('metadata/general/show_menu').text,\n 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,\n- }\n+ },\n+ 'plugins': [{\n+ 'location': 'https://cdn.rawgit.com/TAMU-CPT/blastview/97572a21b7f011c2b4d9a0b5af40e292d694cbef/',\n+ 'name': 'BlastView'\n+ }],\n+ 'plugins_python': ['BlastView'],\n }\n+\n+ plugins = root.find('plugins').attrib\n+ if plugins['GCContent'] == 'True':\n+ extra_data['plugins_python'].append('GCContent')\n+ extra_data['plugins'].append({\n+ 'location': 'https://cdn.rawgit.com/elsiklab/gccontent/5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',\n+ 'name': 'GCContent'\n+ })\n+\n+ if plugins['Bookmarks'] == 'True':\n+ extra_data['plugins'].append({\n+ 'location': 'https://cdn.rawgit.com/TAMU-CPT/bookmarks-jbrowse/5242694120274c86e1ccd5cb0e5e943e78f82393/',\n+ 'name': 'Bookmarks'\n+ })\n+\n+ if plugins['ComboTrackSelector'] == 'True':\n+ extra_data['plugins_python'].append('ComboTrackSelector')\n+ extra_data['plugins'].append({\n+ 'location': 'https://cdn.rawgit.com/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+ 'location': 'https://cdn.rawgit.com/erasche/jbrowse-minimalist-theme/d698718442da306cf87f033c72ddb745f3077775/',\n+ 'name': 'MinimalistTheme'\n+ })\n+ elif plugins['theme'] == 'Dark':\n+ extra_data['plugins'].append({\n+ 'location': 'https://cdn.rawgit.com/erasche/jbrowse-dark-theme/689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',\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+\n for track in root.findall('tracks/track'):\n track_conf = {}\n- track_conf['trackfiles'] = [\n- (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label'])\n- for x in track.findall('files/trackFile')\n- ]\n+ track_conf['trackfiles'] = []\n+\n+ for x in track.findall('files/trackFile'):\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 \n track_conf['category'] = track.attrib['cat']\n track_conf['format'] = track.attrib['format']\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:\n+ except TypeError as te:\n track_conf['style'] = {}\n pass\n track_conf['conf'] = etree_to_dict(track.find('options'))\n@@ -743,4 +945,3 @@\n extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)\n \n jc.add_final_data(extra_data)\n- jc.generate_names()\n" |
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| diff -r b5c5470d7c09 -r ff11d442feed jbrowse.xml --- a/jbrowse.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/jbrowse.xml Wed Nov 15 15:15:27 2017 -0500 |
| [ |
| b'@@ -5,6 +5,7 @@\n </macros>\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n+ <version_command>python jbrowse.py --version</version_command>\n <command><![CDATA[\n \n #if $action.action_select == "create":\n@@ -75,7 +76,29 @@\n <genome>${reference_genome.genomes.fields.path}</genome>\n #else\n #for $genome in $reference_genome.genomes:\n- <genome>$genome</genome>\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 #end if\n </genomes>\n@@ -91,24 +114,55 @@\n <show_menu>${jbgen.show_menu}</show_menu>\n <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>\n </general>\n+ <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>\n </metadata>\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 <files>\n #for $dataset in $track.data_format.annotation:\n- <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />\n+ <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">\n+ <metadata>\n+ <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"\n+ size="${dataset.get_size(nice_size=True)}"\n+ edam_format="${dataset.datatype.edam_format}"\n+ file_ext="${dataset.ext}" />\n+ <history id="${__app__.security.encode_id($dataset.history_id)}"\n+ user_email="${dataset.history.user.email}"\n+ user_id="${dataset.history.user_id}"\n+ display_name="${dataset.history.get_display_name()}"/>\n+ <metadata\n+ #for (key, value) in $dataset.get_metadata().items():\n+ #if "_types" not in $key:\n+ ${key}="${value}"\n+ #end if\n+ #end for\n+ />\n+ <tool\n+ tool_id="${dataset.creating_job.tool_id}"\n+ tool_version="${dataset.creating_job.tool_version}"\n+ />\n+ </metadata>\n+ </trackFile>\n #end for\n </files>\n \n '..b'ct" label="Visual Scaling" name="scale_select2">\n+ <option value="linear" selected="true">Linear</option>\n+ <option value="log">Logarithmic (Dynamically Calculated)</option>\n+ </param>\n <expand macro="color_selection_minmax" />\n <expand macro="track_display" />\n </when>\n+ <when value="rest">\n+ <param type="text" label="REST Endpoint" name="url" />\n+ </when>\n <!--\n <when value="sparql">\n <param type="text" label="SPARQL Server URL" name="url" />\n@@ -497,6 +566,25 @@\n </repeat>\n \n <expand macro="general_options" />\n+ <section name="plugins" title="Plugins" expanded="false">\n+ <param\n+ label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"\n+ help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />\n+ <param\n+ label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"\n+ help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />\n+\n+ <param\n+ label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"\n+ help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />\n+\n+ <param type="select" label="JBrowse Theme" name="theme">\n+ <option value="" selected="True">Default</option>\n+ <option value="Minimalist">Minimalist</option>\n+ <option value="Dark">Dark</option>\n+ </param>\n+ </section>\n+\n <param type="hidden" name="uglyTestingHack" value="" />\n </inputs>\n <outputs>\n@@ -518,7 +606,7 @@\n <param name="gencode" value="11" />\n <param name="standalone" value="Data Directory" />\n <param name="uglyTestingHack" value="enabled" />\n- <output name="output" file="gencode/test.xml" lines_diff="4"/>\n+ <output name="output" file="gencode/test.xml" lines_diff="14"/>\n </test>\n <test>\n <param name="reference_genome|genome_type_select" value="history"/>\n@@ -714,7 +802,7 @@\n </repeat>\n \n <param name="uglyTestingHack" value="enabled" />\n- <output name="output" file="gff3/test.xml" lines_diff="24" />\n+ <output name="output" file="gff3/test.xml" lines_diff="64" />\n </test>\n <test>\n <param name="reference_genome|genome_type_select" value="history"/>\n@@ -777,7 +865,7 @@\n </repeat>\n \n <param name="uglyTestingHack" value="enabled" />\n- <output name="output" file="menus/test.xml" lines_diff="6"/>\n+ <output name="output" file="menus/test.xml" lines_diff="24"/>\n </test>\n <test>\n <param name="reference_genome|genome_type_select" value="history"/>\n@@ -814,7 +902,7 @@\n </repeat>\n \n <param name="uglyTestingHack" value="enabled" />\n- <output name="output" file="track_config/test.xml" lines_diff="6"/>\n+ <output name="output" file="track_config/test.xml" lines_diff="26"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -824,6 +912,12 @@\n JBrowse-in-Galaxy offers a highly configurable, workflow-compatible\n alternative to Trackster.\n \n+Overview\n+--------\n+\n+JBrowse is a fast, embeddable genome browser built completely with\n+JavaScript and HTML5.\n+\n The JBrowse-in-Galaxy (JiG) tool was written to help build complex\n JBrowse installations straight from Galaxy, taking advantage of the\n latest Galaxy features such as dataset collections, sections, and colour\n' |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed macros.xml --- a/macros.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/macros.xml Wed Nov 15 15:15:27 2017 -0500 |
| [ |
| @@ -12,7 +12,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">0.5.3</token> + <token name="@WRAPPER_VERSION@">0.7.0</token> <xml name="stdio"> <stdio> <exit_code range="1:"/> @@ -27,6 +27,43 @@ This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche ]]> </token> + + <xml name="genome_selector" + token_help="" + token_label="Fasta sequences" + token_optional="False" > + <conditional name="reference_genome"> + <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> + <option selected="True" value="indexed">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="indexed"> + <param + help="@HELP@" + label="@LABEL@" + name="genomes" + type="select" + optional="@OPTIONAL@" + > + <options from_data_table="all_fasta"> + <filter column="2" type="sort_by" /> + <validator message="No genomes are available for the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param + format="fasta" + label="@LABEL@" + help="@HELP@" + name="genomes" + type="data" + optional="@OPTIONAL@" + multiple="True" /> + </when> + </conditional> + </xml> + <xml name="auto_manual_tk" token_cond_label="Color" token_cond_name="color" @@ -54,6 +91,14 @@ <option value="force">Force On</option> <option value="always">Always On (ignores URL parameters)</option> </param> + <param type="select" label="Override Apollo Plugins" name="override_apollo_plugins" help="Disable the apollo plugin for this track, this disables the ability to make an annotation from this feature."> + <option value="True">Yes - Override</option> + <option value="False" selected="True">No - Do not Override</option> + </param> + <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality."> + <option value="True">Yes - Override</option> + <option value="False" selected="True">No - Do not Override</option> + </param> </xml> <xml name="jb_color" @@ -179,9 +224,9 @@ <!-- Scaling --> <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution."> - <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option> - <option value="logarithmic">Logarithmic scaling</option> - <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option> + <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> + <option value="logarithmic" selected="false">Logarithmic scaling</option> + <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> </param> <!-- Scaling Bounds --> @@ -219,9 +264,10 @@ </xml> <xml name="track_styling" token_classname="feature" - token_label="name,id" + token_label="product,name,id" token_description="note,description" - token_height="100px"> + token_height="10px" + token_maxheight="600"> <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> <param label="JBrowse style.className" type="text" name="style_classname" @@ -242,6 +288,11 @@ name="style_height" value="@HEIGHT@" help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/> + <param label="JBrowse maxHeight" + type="text" + name="max_height" + value="@MAXHEIGHT@" + help="Maximum height that the track is permitted to reach in pixels."/> </section> </xml> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/bam/test.xml --- a/test-data/bam/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/bam/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -5,6 +5,17 @@ <genomes> <genome>test-data/merlin.fa</genome> </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> </metadata> <tracks> <track cat="Default" format="pileup"> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/blastxml/test.xml --- a/test-data/blastxml/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/blastxml/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -5,6 +5,17 @@ <genomes> <genome>test-data/merlin.fa</genome> </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> </metadata> <tracks> <track cat="Blah" format="blast"> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/bw/data.bw |
| b |
| Binary file test-data/bw/data.bw has changed |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/bw/test.xml --- a/test-data/bw/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/bw/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -5,6 +5,17 @@ <genomes> <genome>test-data/merlin.fa</genome> </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> </metadata> <tracks> <track cat="Scaling" format="wiggle"> @@ -20,6 +31,7 @@ <color_pos>__auto__</color_pos> <color_neg>__auto__</color_neg> <bicolor_pivot>zero</bicolor_pivot> + <scale>linear</scale> </wiggle> </options> </track> @@ -36,6 +48,7 @@ <color_pos>__auto__</color_pos> <color_neg>__auto__</color_neg> <bicolor_pivot>zero</bicolor_pivot> + <scale>linear</scale> </wiggle> </options> </track> @@ -54,6 +67,7 @@ <color_pos>__auto__</color_pos> <color_neg>__auto__</color_neg> <bicolor_pivot>zero</bicolor_pivot> + <scale>linear</scale> </wiggle> </options> </track> @@ -74,6 +88,7 @@ <color_pos>__auto__</color_pos> <color_neg>__auto__</color_neg> <bicolor_pivot>mean</bicolor_pivot> + <scale>linear</scale> </wiggle> </options> </track> @@ -91,6 +106,7 @@ <color_pos>#0000ff</color_pos> <color_neg>#ff0000</color_neg> <bicolor_pivot>mean</bicolor_pivot> + <scale>linear</scale> </wiggle> </options> </track> @@ -108,6 +124,7 @@ <color_pos>#ff0000</color_pos> <color_neg>#0000ff</color_neg> <bicolor_pivot>mean</bicolor_pivot> + <scale>log</scale> </wiggle> </options> </track> @@ -125,6 +142,7 @@ <color_pos>#0000ff</color_pos> <color_neg>#ff0000</color_neg> <bicolor_pivot>100</bicolor_pivot> + <scale>linear</scale> </wiggle> </options> </track> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/gencode/test-1.xml --- a/test-data/gencode/test-1.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/gencode/test-1.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -3,7 +3,27 @@ <metadata> <gencode>1</gencode> <genomes> - <genome>/tmp/tmpPJZIQf/files/000/dataset_1.dat</genome> + <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> </genomes> <general> <defaultLocation></defaultLocation> @@ -17,7 +37,14 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> + <galaxyUrl>http://localhost:8080</galaxyUrl> </metadata> <tracks> </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + theme="" + /> </root> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/gencode/test.xml --- a/test-data/gencode/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/gencode/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -3,7 +3,27 @@ <metadata> <gencode>11</gencode> <genomes> - <genome>/tmp/tmps5cL_a/files/000/dataset_3.dat</genome> + <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> </genomes> <general> <defaultLocation></defaultLocation> @@ -17,7 +37,14 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> + <galaxyUrl>http://localhost:8080</galaxyUrl> </metadata> <tracks> </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + theme="" + /> </root> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/gff3/test.xml --- a/test-data/gff3/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/gff3/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| b'@@ -3,7 +3,27 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome>test-data/merlin.fa</genome>\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 </genomes>\n <general>\n <defaultLocation></defaultLocation>\n@@ -17,22 +37,122 @@\n <show_menu>true</show_menu>\n <hideGenomeOptions>false</hideGenomeOptions>\n </general>\n+ <galaxyUrl>http://localhost:8080</galaxyUrl>\n </metadata>\n <tracks>\n <track cat="Auto Coloured" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>\n+ <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">\n+ <metadata>\n+ <dataset id="fa6d20d0fb68383f" hid="2"\n+ size="2.3 KB"\n+ edam_format="format_1975"\n+ file_ext="gff3" />\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="27"\n+ comment_lines="19"\n+ columns="9"\n+ column_names=""\n+ delimiter="__tc__"\n+ attributes="6"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.4"\n+ />\n+ </metadata>\n+ </trackFile>\n+ <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">\n+ <metadata>\n+ <dataset id="683bc220e21425bb" hid="3"\n+ size="2.3 KB"\n+ edam_format="format_1975"\n+ file_ext="gff3" />\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="27"\n+ comment_lines="19"\n+ columns="9"\n+ column_names=""\n+ delimiter="__tc__"\n+ attributes="6"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.4"\n+ />\n+ </metadata>\n+ </trackFile>\n+ <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff">\n+ <metadata>\n+ <dataset id="a90a30fafe298e1e'..b' </track>\n <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>\n+ <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">\n+ <metadata>\n+ <dataset id="9ce08b2254e4d5ed" hid="7"\n+ size="103.3 KB"\n+ edam_format="format_1975"\n+ file_ext="gff3" />\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="556"\n+ comment_lines="2"\n+ columns="9"\n+ column_names=""\n+ delimiter="__tc__"\n+ attributes="11"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.4"\n+ />\n+ </metadata>\n+ </trackFile>\n </files>\n \n <options>\n <style>\n+ <overridePlugins>False</overridePlugins>\n+ <overrideDraggable>False</overrideDraggable>\n <className>feature</className>\n <description>note,description</description>\n- <label>name,id</label>\n- <height>100px</height>\n+ <label>product,name,id</label>\n+ <height>10px</height>\n+ <maxHeight>600</maxHeight>\n </style>\n <scaling>\n <method>ignore</method>\n@@ -241,15 +523,42 @@\n </track>\n <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>\n+ <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">\n+ <metadata>\n+ <dataset id="80b8022ff3f677b7" hid="8"\n+ size="326 bytes"\n+ edam_format="format_1975"\n+ file_ext="gff3" />\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="3"\n+ comment_lines="3"\n+ columns="9"\n+ column_names=""\n+ delimiter="__tc__"\n+ attributes="4"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.4"\n+ />\n+ </metadata>\n+ </trackFile>\n </files>\n \n <options>\n <style>\n+ <overridePlugins>False</overridePlugins>\n+ <overrideDraggable>False</overrideDraggable>\n <className>feature</className>\n <description>note,description</description>\n- <label>name,id</label>\n- <height>100px</height>\n+ <label>product,name,id</label>\n+ <height>10px</height>\n+ <maxHeight>600</maxHeight>\n </style>\n <scaling>\n <method>ignore</method>\n@@ -268,4 +577,10 @@\n </options>\n </track>\n </tracks>\n+ <plugins\n+ ComboTrackSelector=""\n+ Bookmarks=""\n+ GCContent=""\n+ theme=""\n+ />\n </root>\n' |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/menus/test.xml --- a/test-data/menus/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/menus/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -3,7 +3,27 @@ <metadata> <gencode>11</gencode> <genomes> - <genome>/tmp/tmplFZ5li/files/000/dataset_14.dat</genome> + <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> </genomes> <general> <defaultLocation></defaultLocation> @@ -17,19 +37,47 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> + <galaxyUrl>http://localhost:8080</galaxyUrl> </metadata> <tracks> <track cat="With menu or index" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmplFZ5li/files/000/dataset_15.dat" ext="gff3" label="1.gff" /> + <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_15.dat" ext="gff3" label="1.gff"> + <metadata> + <dataset id="440a6c2b5d9efe20" hid="2" + size="2.3 KB" + edam_format="format_1975" + file_ext="gff3" /> + <history id="8155e4b4bf1581ff" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="hg17" + data_lines="27" + comment_lines="19" + columns="9" + column_names="" + delimiter="__tc__" + attributes="6" + /> + <tool + tool_id="upload1" + tool_version="1.1.4" + /> + </metadata> + </trackFile> </files> <options> <style> + <overridePlugins>False</overridePlugins> + <overrideDraggable>False</overrideDraggable> <className>feature</className> <description>note,description</description> - <label>name,id</label> - <height>100px</height> + <label>product,name,id</label> + <height>10px</height> + <maxHeight>600</maxHeight> </style> <scaling> <method>ignore</method> @@ -62,15 +110,42 @@ </track> <track cat="With menu or index" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmplFZ5li/files/000/dataset_15.dat" ext="gff3" label="1.gff" /> + <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_15.dat" ext="gff3" label="1.gff"> + <metadata> + <dataset id="440a6c2b5d9efe20" hid="2" + size="2.3 KB" + edam_format="format_1975" + file_ext="gff3" /> + <history id="8155e4b4bf1581ff" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="hg17" + data_lines="27" + comment_lines="19" + columns="9" + column_names="" + delimiter="__tc__" + attributes="6" + /> + <tool + tool_id="upload1" + tool_version="1.1.4" + /> + </metadata> + </trackFile> </files> <options> <style> + <overridePlugins>False</overridePlugins> + <overrideDraggable>False</overrideDraggable> <className>feature</className> <description>note,description</description> - <label>name,id</label> - <height>100px</height> + <label>product,name,id</label> + <height>10px</height> + <maxHeight>600</maxHeight> </style> <scaling> <method>ignore</method> @@ -88,4 +163,10 @@ </options> </track> </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + theme="" + /> </root> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/track_config/test.xml --- a/test-data/track_config/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/track_config/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -3,7 +3,27 @@ <metadata> <gencode>11</gencode> <genomes> - <genome>/tmp/tmplFZ5li/files/000/dataset_14.dat</genome> + <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> </genomes> <general> <defaultLocation></defaultLocation> @@ -17,19 +37,47 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> + <galaxyUrl>http://localhost:8080</galaxyUrl> </metadata> <tracks> <track cat="With canvas config" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmplFZ5li/files/000/dataset_15.dat" ext="gff3" label="1.gff" /> + <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_18.dat" ext="gff3" label="1.gff"> + <metadata> + <dataset id="61f03d5eef6f1538" hid="2" + size="2.3 KB" + edam_format="format_1975" + file_ext="gff3" /> + <history id="7b55dbb89df8f4e5" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="hg17" + data_lines="27" + comment_lines="19" + columns="9" + column_names="" + delimiter="__tc__" + attributes="6" + /> + <tool + tool_id="upload1" + tool_version="1.1.4" + /> + </metadata> + </trackFile> </files> <options> <style> + <overridePlugins>False</overridePlugins> + <overrideDraggable>False</overrideDraggable> <className>feature</className> <description>note,description</description> - <label>name,id</label> - <height>100px</height> + <label>product,name,id</label> + <height>10px</height> + <maxHeight>600</maxHeight> </style> <scaling> <method>ignore</method> @@ -47,4 +95,10 @@ </options> </track> </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + theme="" + /> </root> |
| b |
| diff -r b5c5470d7c09 -r ff11d442feed test-data/vcf/test.xml --- a/test-data/vcf/test.xml Wed Sep 13 13:07:20 2017 -0400 +++ b/test-data/vcf/test.xml Wed Nov 15 15:15:27 2017 -0500 |
| b |
| @@ -5,6 +5,17 @@ <genomes> <genome>test-data/merlin.fa</genome> </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> </metadata> <tracks> <track cat="Default" format="vcf"> |