comparison jbrowse.py @ 17:ff11d442feed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

16:b5c5470d7c09

#!/usr/bin/env python
import argparse
import codecs
import copy
import hashlib
import json
import logging
import os
import shutil

import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict

from Bio.Data import CodonTable

logging.basicConfig(level=logging.INFO)
log = logging.getLogger('jbrowse')


class ColorScaling(object):

    COLOR_FUNCTION_TEMPLATE = """

        }};

        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}
        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);
        var blue = parseInt(result[3], 16);
        if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}

            var opacity = (score - ({min})) / (({max}) - ({min}));
            opacity = Math.log10(opacity) + Math.log10({max});
        """,
        'blast': """
            var opacity = 0;
            if(score == 0.0) {
                opacity = 1;
            } else{
                opacity = (20 - Math.log10(score)) / 180;
            }
        """
    }

    BREWER_COLOUR_IDX = 0
    BREWER_COLOUR_SCHEMES = [

    def __init__(self):
        self.brewer_colour_idx = 0

    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'))

    def min_max_gff(self, gff_file):
        min_val = None
        max_val = None
        with open(gff_file, 'r') as handle:

# score comes from feature._parent.get('score') or feature.get('score')

INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))


class JbrowseConnector(object):

    def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
        self.TN_TABLE = {
            'gff3': '--gff',

                os.makedirs(self.outdir)
            except OSError:
                # Ignore if the folder exists
                pass

        self.process_genomes()
        self.update_gencode()

    def update_gencode(self):
        table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]

    def _jbrowse_bin(self, command):
        return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))

    def process_genomes(self):
        for genome_path in self.genome_paths:
            self.subprocess_check_call([
                'perl', self._jbrowse_bin('prepare-refseqs.pl'),
                '--fasta', genome_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:
            # No tracks to index, index only the refseq
            args += ['--tracks', 'DNA']

        self.subprocess_check_call(args)

    def _add_json(self, json_data):

        cmd = [
            'perl', self._jbrowse_bin('add-json.pl'),
            json.dumps(json_data),
            os.path.join('data', 'trackList.json')
        ]

               '--gff', gff3,
               '--trackLabel', trackData['label'],
               '--key', trackData['key'],
               '--clientConfig', json.dumps(clientConfig),
               '--config', json.dumps(config),
               '--trackType', 'JBrowse/View/Track/CanvasFeatures'
               ]

        # className in --clientConfig is ignored, it needs to be set with --className
        if 'className' in trackData['style']:
            cmd += ['--className', trackData['style']['className']]

        if 'min' in wiggleOpts and 'max' in wiggleOpts:
            trackData['min_score'] = wiggleOpts['min']
            trackData['max_score'] = wiggleOpts['max']
        else:
            trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')

        self._add_track_json(trackData)

    def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
        dest = os.path.join('data', 'raw', trackData['label'] + '.bam')

            "type": "JBrowse/View/Track/HTMLVariants",
            "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
        })
        self._add_track_json(trackData)

    def add_features(self, data, format, trackData, gffOpts, **kwargs):
        cmd = [
            'perl', self._jbrowse_bin('flatfile-to-json.pl'),
            self.TN_TABLE.get(format, 'gff'),
            data,
            '--trackLabel', trackData['label'],

        cmd += [
            '--trackType', gffOpts['trackType']
        ]

        cmd.extend(['--config', json.dumps(config)])

        self.subprocess_check_call(cmd)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

    def process_annotations(self, track):
        outputTrackConfig = {
            'style': {
                'label': track['style'].get('label', 'description'),
                'className': track['style'].get('className', 'feature'),
                'description': track['style'].get('description', ''),
            },
            'category': track['category'],
        }

        mapped_chars = {
            '>': '__gt__',
            '<': '__lt__',

            '}': '__cc__',
            '@': '__at__',
            '#': '__pd__'
        }

        for i, (dataset_path, dataset_ext, track_human_label) 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)
            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

            # Colour parsing is complex due to different track types having
            # different colour options.
            colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
            # This used to be done with a dict.update() call, however that wiped out any previous style settings...

            # import pprint; pprint.pprint(track)
            # import sys; sys.exit()
            if dataset_ext in ('gff', 'gff3', 'bed'):
                self.add_features(dataset_path, dataset_ext, outputTrackConfig,
                                  track['conf']['options']['gff'])
            elif dataset_ext == 'bigwig':
                self.add_bigwig(dataset_path, outputTrackConfig,
                                track['conf']['options']['wiggle'])
            elif dataset_ext == 'bam':
                real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
                if not isinstance(real_indexes, list):
                    # <bam_indices>
                    #  <bam_index>/path/to/a.bam.bai</bam_index>

                    # becomes a list. Fun!
                    real_indexes = [real_indexes]

                self.add_bam(dataset_path, outputTrackConfig,
                             track['conf']['options']['pileup'],
                             bam_index=real_indexes[i])
            elif dataset_ext == 'blastxml':
                self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
            elif dataset_ext == 'vcf':
                self.add_vcf(dataset_path, outputTrackConfig)

            # Return non-human label for use in other fields
            yield outputTrackConfig['label']

    def add_final_data(self, data):

        generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
        generalData['show_nav'] = (data['general']['show_nav'] == 'true')
        generalData['show_overview'] = (data['general']['show_overview'] == 'true')
        generalData['show_menu'] = (data['general']['show_menu'] == 'true')
        generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')

        viz_data.update(generalData)
        self._add_json(viz_data)

    def clone_jbrowse(self, jbrowse_dir, destination):
        """Clone a JBrowse directory into a destination directory.
        """
        # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks

        log.debug(' '.join(cmd))
        subprocess.check_call(cmd)

        # http://unix.stackexchange.com/a/38691/22785
        # JBrowse releases come with some broken symlinks
        cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
        log.debug(' '.join(cmd))
        subprocess.check_call(cmd)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')

    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')
    args = parser.parse_args()

    tree = ET.parse(args.xml.name)
    root = tree.getroot()

    jc = JbrowseConnector(
        jbrowse=args.jbrowse,
        outdir=args.outdir,
        genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')],
        standalone=args.standalone,
        gencode=root.find('metadata/gencode').text
    )

    extra_data = {

            'show_tracklist': root.find('metadata/general/show_tracklist').text,
            'show_nav': root.find('metadata/general/show_nav').text,
            '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,
        }
    }
    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['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:
            track_conf['style'] = {}
            pass
        track_conf['conf'] = etree_to_dict(track.find('options'))
        keys = jc.process_annotations(track_conf)

        for key in keys:
            extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)

    jc.add_final_data(extra_data)
    jc.generate_names()

17:ff11d442feed

#!/usr/bin/env python
import argparse
import binascii
import copy
import datetime
import hashlib
import json
import logging
import os
import shutil

import tempfile
import xml.etree.ElementTree as ET
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):

    COLOR_FUNCTION_TEMPLATE = """

        }};

        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);
        var blue = parseInt(result[3], 16);
        if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}

            var opacity = (score - ({min})) / (({max}) - ({min}));
            opacity = Math.log10(opacity) + Math.log10({max});
        """,
        'blast': """
            var opacity = 0;
            if(score == 0.0) {{
                opacity = 1;
            }} else {{
                opacity = (20 - Math.log10(score)) / 180;
            }}
        """
    }

    BREWER_COLOUR_IDX = 0
    BREWER_COLOUR_SCHEMES = [

    def __init__(self):
        self.brewer_colour_idx = 0

    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', binascii.unhexlify(hexstr))

    def min_max_gff(self, gff_file):
        min_val = None
        max_val = None
        with open(gff_file, 'r') as handle:

# score comes from feature._parent.get('score') or feature.get('score')

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):
        self.TN_TABLE = {
            'gff3': '--gff',

                os.makedirs(self.outdir)
            except OSError:
                # 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()

    def update_gencode(self):
        table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]

    def _jbrowse_bin(self, command):
        return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))

    def process_genomes(self):
        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_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:
            # No tracks to index, index only the refseq
            args += ['--tracks', 'DNA']

        self.subprocess_check_call(args)

    def _add_json(self, json_data):
        cmd = [
            'perl', self._jbrowse_bin('add-json.pl'),
            json.dumps(json_data),
            os.path.join('data', 'trackList.json')
        ]

               '--gff', gff3,
               '--trackLabel', trackData['label'],
               '--key', trackData['key'],
               '--clientConfig', json.dumps(clientConfig),
               '--config', json.dumps(config),
               '--trackType', 'BlastView/View/Track/CanvasFeatures'
               ]

        # className in --clientConfig is ignored, it needs to be set with --className
        if 'className' in trackData['style']:
            cmd += ['--className', trackData['style']['className']]

        if 'min' in wiggleOpts and 'max' in wiggleOpts:
            trackData['min_score'] = wiggleOpts['min']
            trackData['max_score'] = wiggleOpts['max']
        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):
        dest = os.path.join('data', 'raw', trackData['label'] + '.bam')

            "type": "JBrowse/View/Track/HTMLVariants",
            "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
        })
        self._add_track_json(trackData)

    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'),
            data,
            '--trackLabel', trackData['label'],

        cmd += [
            '--trackType', gffOpts['trackType']
        ]

        if metadata:
            config.update({'metadata': metadata})
        cmd.extend(['--config', json.dumps(config)])

        self.subprocess_check_call(cmd)

        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', ''),
            },
            'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
            'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
            'maxHeight': track['style'].get('maxHeight', '600'),
            'category': category,
        }

        mapped_chars = {
            '>': '__gt__',
            '<': '__lt__',

            '}': '__cc__',
            '@': '__at__',
            '#': '__pd__'
        }

        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', category, track_human_label)
            outputTrackConfig['key'] = track_human_label
            # 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.
            colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
            # This used to be done with a dict.update() call, however that wiped out any previous style settings...

            # import pprint; pprint.pprint(track)
            # import sys; sys.exit()
            if dataset_ext in ('gff', 'gff3', 'bed'):
                self.add_features(dataset_path, dataset_ext, outputTrackConfig,
                                  track['conf']['options']['gff'], metadata=extra_metadata)
            elif dataset_ext == 'bigwig':
                self.add_bigwig(dataset_path, outputTrackConfig,
                                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):
                    # <bam_indices>
                    #  <bam_index>/path/to/a.bam.bai</bam_index>

                    # becomes a list. Fun!
                    real_indexes = [real_indexes]

                self.add_bam(dataset_path, outputTrackConfig,
                             track['conf']['options']['pileup'],
                             bam_index=real_indexes[i], metadata=extra_metadata)
            elif dataset_ext == 'blastxml':
                self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'], metadata=extra_metadata)
            elif dataset_ext == 'vcf':
                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']

    def add_final_data(self, data):

        generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
        generalData['show_nav'] = (data['general']['show_nav'] == 'true')
        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.
        """
        # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks

        log.debug(' '.join(cmd))
        subprocess.check_call(cmd)

        # http://unix.stackexchange.com/a/38691/22785
        # JBrowse releases come with some broken symlinks
        cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
        log.debug(' '.join(cmd))
        symlinks = subprocess.check_output(cmd)
        for i in symlinks:
            try:
                os.unlink(i)
            except OSError:
                pass


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')

    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)
    root = tree.getroot()

    jc = JbrowseConnector(
        jbrowse=args.jbrowse,
        outdir=args.outdir,
        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
    )

    extra_data = {

            'show_tracklist': root.find('metadata/general/show_tracklist').text,
            'show_nav': root.find('metadata/general/show_nav').text,
            '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'] = []

        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 as te:
            track_conf['style'] = {}
            pass
        track_conf['conf'] = etree_to_dict(track.find('options'))
        keys = jc.process_annotations(track_conf)

        for key in keys:
            extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)

    jc.add_final_data(extra_data)