# HG changeset patch
# User iuc
# Date 1510776927 18000
# Node ID ff11d442feedce38938c803f83f92a24c8a641a3
# Parent  b5c5470d7c0936706bf5713f5b282b7b3528ad58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

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
@@ -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.
+#
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)
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))
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
@@ -1,7 +1,8 @@
 #!/usr/bin/env python
 import argparse
-import codecs
+import binascii
 import copy
+import datetime
 import hashlib
 import json
 import logging
@@ -14,9 +15,10 @@
 from collections import defaultdict
 
 from Bio.Data import CodonTable
-
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger('jbrowse')
+TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
+GALAXY_INFRASTRUCTURE_URL = None
 
 
 class ColorScaling(object):
@@ -63,6 +65,7 @@
         var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
         var score = (search_up(feature, 'score') || search_down(feature, 'score'));
         {opacity}
+        if(score === undefined){{ opacity = 1; }}
         var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
         var red = parseInt(result[1], 16);
         var green = parseInt(result[2], 16);
@@ -82,11 +85,11 @@
         """,
         'blast': """
             var opacity = 0;
-            if(score == 0.0) {
+            if(score == 0.0) {{
                 opacity = 1;
-            } else{
+            }} else {{
                 opacity = (20 - Math.log10(score)) / 180;
-            }
+            }}
         """
     }
 
@@ -128,7 +131,7 @@
 
     def rgb_from_hex(self, hexstr):
         # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
-        return struct.unpack('BBB', codecs.decode(hexstr, 'hex'))
+        return struct.unpack('BBB', binascii.unhexlify(hexstr))
 
     def min_max_gff(self, gff_file):
         min_val = None
@@ -285,6 +288,44 @@
 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
 
 
+def metadata_from_node(node):
+    metadata = {}
+    try:
+        if len(node.findall('dataset')) != 1:
+            # exit early
+            return metadata
+    except Exception:
+        return {}
+
+    for (key, value) in node.findall('dataset')[0].attrib.items():
+        metadata['dataset_%s' % key] = value
+
+    for (key, value) in node.findall('history')[0].attrib.items():
+        metadata['history_%s' % key] = value
+
+    for (key, value) in node.findall('metadata')[0].attrib.items():
+        metadata['metadata_%s' % key] = value
+
+    for (key, value) in node.findall('tool')[0].attrib.items():
+        metadata['tool_%s' % key] = value
+
+    # Additional Mappings applied:
+    metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext'])
+    metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email'])
+    metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
+        galaxy=GALAXY_INFRASTRUCTURE_URL,
+        encoded_hist_id=metadata['history_id'],
+        hist_name=metadata['history_display_name']
+    )
+    metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
+        galaxy=GALAXY_INFRASTRUCTURE_URL,
+        encoded_id=metadata['dataset_id'],
+        tool_id=metadata['tool_tool_id'],
+        tool_version=metadata['tool_tool_version'],
+    )
+    return metadata
+
+
 class JbrowseConnector(object):
 
     def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
@@ -312,6 +353,12 @@
                 # Ignore if the folder exists
                 pass
 
+            try:
+                os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
+            except OSError:
+                # Ignore if the folder exists
+                pass
+
         self.process_genomes()
         self.update_gencode()
 
@@ -338,21 +385,20 @@
         return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
 
     def process_genomes(self):
-        for genome_path in self.genome_paths:
+        for genome_node in self.genome_paths:
+            # TODO: Waiting on https://github.com/GMOD/jbrowse/pull/884
             self.subprocess_check_call([
                 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
-                '--fasta', genome_path])
+                '--fasta', genome_node['path']])
 
     def generate_names(self):
         # Generate names
-
         args = [
             'perl', self._jbrowse_bin('generate-names.pl'),
             '--hashBits', '16'
         ]
 
         tracks = ','.join(self.tracksToIndex)
-
         if tracks:
             args += ['--tracks', tracks]
         else:
@@ -362,7 +408,6 @@
         self.subprocess_check_call(args)
 
     def _add_json(self, json_data):
-
         cmd = [
             'perl', self._jbrowse_bin('add-json.pl'),
             json.dumps(json_data),
@@ -421,7 +466,7 @@
                '--key', trackData['key'],
                '--clientConfig', json.dumps(clientConfig),
                '--config', json.dumps(config),
-               '--trackType', 'JBrowse/View/Track/CanvasFeatures'
+               '--trackType', 'BlastView/View/Track/CanvasFeatures'
                ]
 
         # className in --clientConfig is ignored, it needs to be set with --className
@@ -455,6 +500,8 @@
         else:
             trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
 
+        trackData['scale'] = wiggleOpts['scale']
+
         self._add_track_json(trackData)
 
     def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
@@ -506,7 +553,7 @@
         })
         self._add_track_json(trackData)
 
-    def add_features(self, data, format, trackData, gffOpts, **kwargs):
+    def add_features(self, data, format, trackData, gffOpts, metadata=None, **kwargs):
         cmd = [
             'perl', self._jbrowse_bin('flatfile-to-json.pl'),
             self.TN_TABLE.get(format, 'gff'),
@@ -549,6 +596,8 @@
             '--trackType', gffOpts['trackType']
         ]
 
+        if metadata:
+            config.update({'metadata': metadata})
         cmd.extend(['--config', json.dumps(config)])
 
         self.subprocess_check_call(cmd)
@@ -556,14 +605,32 @@
         if gffOpts.get('index', 'false') == 'true':
             self.tracksToIndex.append("%s" % trackData['label'])
 
+    def add_rest(self, url, trackData):
+        data = {
+            "label": trackData['label'],
+            "key": trackData['key'],
+            "category": trackData['category'],
+            "type": "JBrowse/View/Track/HTMLFeatures",
+            "storeClass": "JBrowse/Store/SeqFeature/REST",
+            "baseUrl": url,
+            "query": {
+                "organism": "tyrannosaurus"
+            }
+        }
+        self._add_track_json(data)
+
     def process_annotations(self, track):
+        category = track['category'].replace('__pd__date__pd__', TODAY)
         outputTrackConfig = {
             'style': {
                 'label': track['style'].get('label', 'description'),
                 'className': track['style'].get('className', 'feature'),
                 'description': track['style'].get('description', ''),
             },
-            'category': track['category'],
+            'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
+            'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
+            'maxHeight': track['style'].get('maxHeight', '600'),
+            'category': category,
         }
 
         mapped_chars = {
@@ -579,15 +646,26 @@
             '#': '__pd__'
         }
 
-        for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
+        for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
             # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
             for key, value in mapped_chars.items():
                 track_human_label = track_human_label.replace(value, key)
 
-            log.info('Processing %s / %s', track['category'], track_human_label)
+            log.info('Processing %s / %s', category, track_human_label)
             outputTrackConfig['key'] = track_human_label
-            hashData = [dataset_path, track_human_label, track['category']]
-            outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i
+            # We add extra data to hash for the case of REST + SPARQL.
+            try:
+                rest_url = track['conf']['options']['url']
+            except KeyError:
+                rest_url = ''
+
+            # I chose to use track['category'] instead of 'category' here. This
+            # is intentional. This way re-running the tool on a different date
+            # will not generate different hashes and make comparison of outputs
+            # much simpler.
+            hashData = [dataset_path, track_human_label, track['category'], rest_url]
+            hashData = '|'.join(hashData).encode('utf-8')
+            outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
 
             # Colour parsing is complex due to different track types having
             # different colour options.
@@ -608,10 +686,10 @@
             # import sys; sys.exit()
             if dataset_ext in ('gff', 'gff3', 'bed'):
                 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
-                                  track['conf']['options']['gff'])
+                                  track['conf']['options']['gff'], metadata=extra_metadata)
             elif dataset_ext == 'bigwig':
                 self.add_bigwig(dataset_path, outputTrackConfig,
-                                track['conf']['options']['wiggle'])
+                                track['conf']['options']['wiggle'], metadata=extra_metadata)
             elif dataset_ext == 'bam':
                 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
                 if not isinstance(real_indexes, list):
@@ -626,11 +704,15 @@
 
                 self.add_bam(dataset_path, outputTrackConfig,
                              track['conf']['options']['pileup'],
-                             bam_index=real_indexes[i])
+                             bam_index=real_indexes[i], metadata=extra_metadata)
             elif dataset_ext == 'blastxml':
-                self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
+                self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'], metadata=extra_metadata)
             elif dataset_ext == 'vcf':
-                self.add_vcf(dataset_path, outputTrackConfig)
+                self.add_vcf(dataset_path, outputTrackConfig, metadata=extra_metadata)
+            elif dataset_ext == 'rest':
+                self.add_rest(track['conf']['options']['url'], outputTrackConfig, metadata=extra_metadata)
+            else:
+                log.warn('Do not know how to handle %s', dataset_ext)
 
             # Return non-human label for use in other fields
             yield outputTrackConfig['label']
@@ -659,10 +741,65 @@
         generalData['show_overview'] = (data['general']['show_overview'] == 'true')
         generalData['show_menu'] = (data['general']['show_menu'] == 'true')
         generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
+        generalData['plugins'] = data['plugins']
 
         viz_data.update(generalData)
         self._add_json(viz_data)
 
+        if 'GCContent' in data['plugins_python']:
+            self._add_track_json({
+                "storeClass": "JBrowse/Store/SeqFeature/SequenceChunks",
+                "type": "GCContent/View/Track/GCContentXY",
+                "label": "GCContentXY",
+                "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
+                "bicolor_pivot": 0.5
+                # TODO: Expose params for everyone.
+            })
+
+        if 'ComboTrackSelector' in data['plugins_python']:
+            with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
+                trackListJson = json.load(handle)
+                trackListJson.update({
+                    "trackSelector": {
+                        "renameFacets": {
+                            "tool_tool": "Tool ID",
+                            "tool_tool_id": "Tool ID",
+                            "tool_tool_version": "Tool Version",
+                            "dataset_edam_format": "EDAM",
+                            "dataset_size": "Size",
+                            "history_display_name": "History Name",
+                            "history_user_email": "Owner",
+                            "metadata_dbkey": "Dbkey",
+                        },
+                        "displayColumns": [
+                            "key",
+                            "tool_tool",
+                            "tool_tool_version",
+                            "dataset_edam_format",
+                            "dataset_size",
+                            "history_display_name",
+                            "history_user_email",
+                            "metadata_dbkey",
+                        ],
+                        "type": "Faceted",
+                        "title": ["Galaxy Metadata"],
+                        "escapeHTMLInData": False
+                    },
+                    "trackMetadata": {
+                        "indexFacets": [
+                            "category",
+                            "key",
+                            "tool_tool_id",
+                            "tool_tool_version",
+                            "dataset_edam_format",
+                            "history_user_email",
+                            "history_display_name"
+                        ]
+                    }
+                })
+                with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
+                    json.dump(trackListJson, handle)
+
     def clone_jbrowse(self, jbrowse_dir, destination):
         """Clone a JBrowse directory into a destination directory.
         """
@@ -677,9 +814,14 @@
 
         # http://unix.stackexchange.com/a/38691/22785
         # JBrowse releases come with some broken symlinks
-        cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
+        cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
         log.debug(' '.join(cmd))
-        subprocess.check_call(cmd)
+        symlinks = subprocess.check_output(cmd)
+        for i in symlinks:
+            try:
+                os.unlink(i)
+            except OSError:
+                pass
 
 
 if __name__ == '__main__':
@@ -689,6 +831,7 @@
     parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
     parser.add_argument('--outdir', help='Output directory', default='out')
     parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
+    parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.7.0")
     args = parser.parse_args()
 
     tree = ET.parse(args.xml.name)
@@ -697,7 +840,13 @@
     jc = JbrowseConnector(
         jbrowse=args.jbrowse,
         outdir=args.outdir,
-        genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')],
+        genomes=[
+            {
+                'path': os.path.realpath(x.attrib['path']),
+                'meta': metadata_from_node(x.find('metadata'))
+            }
+            for x in root.findall('metadata/genomes/genome')
+        ],
         standalone=args.standalone,
         gencode=root.find('metadata/gencode').text
     )
@@ -719,21 +868,74 @@
             'show_overview': root.find('metadata/general/show_overview').text,
             'show_menu': root.find('metadata/general/show_menu').text,
             'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
-        }
+        },
+        'plugins': [{
+            'location': 'https://cdn.rawgit.com/TAMU-CPT/blastview/97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
+            'name': 'BlastView'
+        }],
+        'plugins_python': ['BlastView'],
     }
+
+    plugins = root.find('plugins').attrib
+    if plugins['GCContent'] == 'True':
+        extra_data['plugins_python'].append('GCContent')
+        extra_data['plugins'].append({
+            'location': 'https://cdn.rawgit.com/elsiklab/gccontent/5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
+            'name': 'GCContent'
+        })
+
+    if plugins['Bookmarks'] == 'True':
+        extra_data['plugins'].append({
+            'location': 'https://cdn.rawgit.com/TAMU-CPT/bookmarks-jbrowse/5242694120274c86e1ccd5cb0e5e943e78f82393/',
+            'name': 'Bookmarks'
+        })
+
+    if plugins['ComboTrackSelector'] == 'True':
+        extra_data['plugins_python'].append('ComboTrackSelector')
+        extra_data['plugins'].append({
+            'location': 'https://cdn.rawgit.com/Arabidopsis-Information-Portal/ComboTrackSelector/52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57',
+            'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
+            'name': 'ComboTrackSelector'
+        })
+
+    if plugins['theme'] == 'Minimalist':
+        extra_data['plugins'].append({
+            'location': 'https://cdn.rawgit.com/erasche/jbrowse-minimalist-theme/d698718442da306cf87f033c72ddb745f3077775/',
+            'name': 'MinimalistTheme'
+        })
+    elif plugins['theme'] == 'Dark':
+        extra_data['plugins'].append({
+            'location': 'https://cdn.rawgit.com/erasche/jbrowse-dark-theme/689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
+            'name': 'DarkTheme'
+        })
+
+    GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text
+    # Sometimes this comes as `localhost` without a protocol
+    if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):
+        # so we'll prepend `http://` and hope for the best. Requests *should*
+        # be GET and not POST so it should redirect OK
+        GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL
+
     for track in root.findall('tracks/track'):
         track_conf = {}
-        track_conf['trackfiles'] = [
-            (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label'])
-            for x in track.findall('files/trackFile')
-        ]
+        track_conf['trackfiles'] = []
+
+        for x in track.findall('files/trackFile'):
+            metadata = metadata_from_node(x.find('metadata'))
+
+            track_conf['trackfiles'].append((
+                os.path.realpath(x.attrib['path']),
+                x.attrib['ext'],
+                x.attrib['label'],
+                metadata
+            ))
 
         track_conf['category'] = track.attrib['cat']
         track_conf['format'] = track.attrib['format']
         try:
             # Only pertains to gff3 + blastxml. TODO?
             track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
-        except TypeError:
+        except TypeError as te:
             track_conf['style'] = {}
             pass
         track_conf['conf'] = etree_to_dict(track.find('options'))
@@ -743,4 +945,3 @@
             extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
 
     jc.add_final_data(extra_data)
-    jc.generate_names()
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
@@ -5,6 +5,7 @@
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
+  <version_command>python jbrowse.py --version</version_command>
   <command><![CDATA[
 
 #if $action.action_select == "create":
@@ -75,7 +76,29 @@
               <genome>${reference_genome.genomes.fields.path}</genome>
             #else
               #for $genome in $reference_genome.genomes:
-                  <genome>$genome</genome>
+                  <genome path="$genome">
+                    <metadata>
+                      <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
+                          size="${genome.get_size(nice_size=True)}"
+                          edam_format="${genome.datatype.edam_format}"
+                          file_ext="${genome.ext}" />
+                      <history id="${__app__.security.encode_id($genome.history_id)}"
+                          user_email="${genome.history.user.email}"
+                          user_id="${genome.history.user_id}"
+                          display_name="${genome.history.get_display_name()}"/>
+                      <metadata
+                          #for (key, value) in $genome.get_metadata().items():
+                          #if "_types" not in $key:
+                          ${key}="${value}"
+                          #end if
+                          #end for
+                          />
+                      <tool
+                          tool_id="${genome.creating_job.tool_id}"
+                          tool_version="${genome.creating_job.tool_version}"
+                          />
+                    </metadata>
+                  </genome>
               #end for
             #end if
         </genomes>
@@ -91,24 +114,55 @@
             <show_menu>${jbgen.show_menu}</show_menu>
             <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
         </general>
+        <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
     </metadata>
     <tracks>
         #for $tg in $track_groups:
         #for $track in $tg.data_tracks:
+        #if $track.data_format.data_format_select == "rest":
+        <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
+            <url>${track.data_format.url}</url>
+        </track>
+        #else:
         <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
             <files>
               #for $dataset in $track.data_format.annotation:
-              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
+              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
+                <metadata>
+                  <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
+                      size="${dataset.get_size(nice_size=True)}"
+                      edam_format="${dataset.datatype.edam_format}"
+                      file_ext="${dataset.ext}" />
+                  <history id="${__app__.security.encode_id($dataset.history_id)}"
+                      user_email="${dataset.history.user.email}"
+                      user_id="${dataset.history.user_id}"
+                      display_name="${dataset.history.get_display_name()}"/>
+                  <metadata
+                    #for (key, value) in $dataset.get_metadata().items():
+                    #if "_types" not in $key:
+                      ${key}="${value}"
+                    #end if
+                    #end for
+                      />
+                  <tool
+                      tool_id="${dataset.creating_job.tool_id}"
+                      tool_version="${dataset.creating_job.tool_version}"
+                      />
+                </metadata>
+              </trackFile>
               #end for
             </files>
 
             <options>
             #if str($track.data_format.data_format_select) == "gene_calls" or  str($track.data_format.data_format_select) == "blast":
                 <style>
+                    <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
+                    <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
                     <className>${track.data_format.jbstyle.style_classname}</className>
                     <description>${track.data_format.jbstyle.style_description}</description>
                     <label>${track.data_format.jbstyle.style_label}</label>
                     <height>${track.data_format.jbstyle.style_height}</height>
+                    <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
                 </style>
                 <scaling>
                   #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
@@ -177,6 +231,7 @@
                     <min>${track.data_format.scaling.minimum}</min>
                     <max>${track.data_format.scaling.maximum}</max>
                   #end if
+                  <scale>${track.data_format.scale_select2}</scale>
 
                   ## Wiggle tracks need special color config
                   #if str($track.data_format.jbcolor.color.color_select) != "automatic":
@@ -247,11 +302,17 @@
             #end if
             </options>
         </track>
+        #end if
         #end for
         #end for
     </tracks>
-</root>
-]]></configfile>
+    <plugins
+        ComboTrackSelector="${plugins.ComboTrackSelector}"
+        Bookmarks="${plugins.Bookmarks}"
+        GCContent="${plugins.GCContent}"
+        theme="${plugins.theme}"
+        />
+</root>]]></configfile>
   </configfiles>
   <inputs>
     <conditional name="reference_genome">
@@ -284,7 +345,6 @@
 
     <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>
 
-
     <param label="Genetic Code" name="gencode" type="select">
       <option value="1">1. The Standard Code</option>
       <option value="2">2. The Vertebrate Mitochondrial Code</option>
@@ -325,15 +385,16 @@
                name="category"
                type="text"
                value="Default"
-               help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
+               help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
     <repeat name="data_tracks" title="Annotation Track">
-        <conditional name="data_format">
+        <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="pileup">BAM Pileups</option>
                 <option value="blast">Blast XML</option>
                 <option value="wiggle">BigWig XY</option>
                 <option value="vcf">VCF SNPs</option>
+                <option value="rest">REST Endpoint</option>
                 <!--<option value="sparql">SPARQL</option>-->
             </param>
             <when value="blast">
@@ -377,7 +438,7 @@
             </when>
             <when value="gene_calls">
                 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
-                <conditional name="match_part">
+                <conditional name="match_part" label="match/match_part data">
                     <param label="This is match/match_part data"
                            type="boolean"
                            name="match_part_select"
@@ -400,6 +461,7 @@
                     <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
                         <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
                         <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
+                        <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option>
                     </param>
                     <when value="JBrowse/View/Track/CanvasFeatures">
                         <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
@@ -466,7 +528,7 @@
                        truevalue="true"
                        falsevalue="false" />
 
-                <conditional name="scaling">
+                <conditional name="scaling" label="Scaling">
                     <param type="select" label="Track Scaling" name="scale_select">
                         <option value="auto_local">Autoscale (local)</option>
                         <option value="auto_global" selected="true">Autoscale (global)</option>
@@ -481,9 +543,16 @@
                             type="integer" value="100" />
                     </when>
                 </conditional>
+                <param type="select" label="Visual Scaling" name="scale_select2">
+                    <option value="linear" selected="true">Linear</option>
+                    <option value="log">Logarithmic (Dynamically Calculated)</option>
+                </param>
                 <expand macro="color_selection_minmax" />
                 <expand macro="track_display" />
             </when>
+            <when value="rest">
+                <param type="text" label="REST Endpoint" name="url" />
+            </when>
             <!--
             <when value="sparql">
                 <param type="text" label="SPARQL Server URL" name="url" />
@@ -497,6 +566,25 @@
     </repeat>
 
     <expand macro="general_options" />
+    <section name="plugins" title="Plugins" expanded="false">
+        <param
+            label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
+            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" />
+        <param
+            label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
+            help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />
+
+        <param
+            label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
+            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)." />
+
+        <param type="select" label="JBrowse Theme" name="theme">
+            <option value="" selected="True">Default</option>
+            <option value="Minimalist">Minimalist</option>
+            <option value="Dark">Dark</option>
+        </param>
+    </section>
+
     <param type="hidden" name="uglyTestingHack" value="" />
   </inputs>
   <outputs>
@@ -518,7 +606,7 @@
       <param name="gencode" value="11" />
       <param name="standalone" value="Data Directory" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test.xml" lines_diff="4"/>
+      <output name="output" file="gencode/test.xml" lines_diff="14"/>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -714,7 +802,7 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="24" />
+      <output name="output" file="gff3/test.xml" lines_diff="64" />
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -777,7 +865,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="menus/test.xml" lines_diff="6"/>
+        <output name="output" file="menus/test.xml" lines_diff="24"/>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -814,7 +902,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="track_config/test.xml" lines_diff="6"/>
+        <output name="output" file="track_config/test.xml" lines_diff="26"/>
     </test>
   </tests>
   <help><![CDATA[
@@ -824,6 +912,12 @@
 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
 alternative to Trackster.
 
+Overview
+--------
+
+JBrowse is a fast, embeddable genome browser built completely with
+JavaScript and HTML5.
+
 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
 JBrowse installations straight from Galaxy, taking advantage of the
 latest Galaxy features such as dataset collections, sections, and colour
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>
 
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
@@ -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">
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
@@ -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">
diff -r b5c5470d7c09 -r ff11d442feed test-data/bw/data.bw
Binary file test-data/bw/data.bw has changed
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
@@ -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>
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
@@ -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>
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
@@ -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>
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
@@ -3,7 +3,27 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-                  <genome>test-data/merlin.fa</genome>
+                  <genome path="/tmp/tmpnh6QWY/files/000/dataset_5.dat">
+                    <metadata>
+                      <dataset id="7b55dbb89df8f4e5" hid="1"
+                          size="171.6 KB"
+                          edam_format="format_1929"
+                          file_ext="fasta" />
+                      <history id="54f2a3a23292eb07"
+                          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>
@@ -17,22 +37,122 @@
             <show_menu>true</show_menu>
             <hideGenomeOptions>false</hideGenomeOptions>
         </general>
+        <galaxyUrl>http://localhost:8080</galaxyUrl>
     </metadata>
     <tracks>
         <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">
+                <metadata>
+                  <dataset id="fa6d20d0fb68383f" hid="2"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">
+                <metadata>
+                  <dataset id="683bc220e21425bb" hid="3"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff">
+                <metadata>
+                  <dataset id="a90a30fafe298e1e" hid="4"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_9.dat" ext="gff3" label="D.gff">
+                <metadata>
+                  <dataset id="b842d972534ccb3e" hid="5"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>
@@ -51,15 +171,42 @@
         </track>
         <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>
@@ -78,15 +225,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>score</method>
@@ -111,15 +285,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>score</method>
@@ -144,15 +345,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>score</method>
@@ -179,15 +407,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      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>score</method>
@@ -214,15 +469,42 @@
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
+                <metadata>
+                  <dataset id="9ce08b2254e4d5ed" hid="7"
+                      size="103.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="556"
+                      comment_lines="2"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="11"
+                      />
+                  <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>
@@ -241,15 +523,42 @@
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">
+                <metadata>
+                  <dataset id="80b8022ff3f677b7" hid="8"
+                      size="326 bytes"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="3"
+                      comment_lines="3"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="4"
+                      />
+                  <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>
@@ -268,4 +577,10 @@
             </options>
         </track>
     </tracks>
+    <plugins
+        ComboTrackSelector=""
+        Bookmarks=""
+        GCContent=""
+        theme=""
+        />
 </root>
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
@@ -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>
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
@@ -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>
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
@@ -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">