comparison jbrowse.py @ 16:b5c5470d7c09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5

15:4e11a688a635

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

    def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
        dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
        cmd = ['ln', data, dest]
        self.subprocess_check_call(cmd)

        url = os.path.join('raw', trackData['label'] + '.bw')
        trackData.update({
            "urlTemplate": url,

                'description': track['style'].get('description', ''),
            },
            'category': track['category'],
        }

        for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
            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

16:b5c5470d7c09

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

    def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
        dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
        cmd = ['ln', '-s', data, dest]
        self.subprocess_check_call(cmd)

        url = os.path.join('raw', trackData['label'] + '.bw')
        trackData.update({
            "urlTemplate": url,

                'description': track['style'].get('description', ''),
            },
            'category': track['category'],
        }

        mapped_chars = {
            '>': '__gt__',
            '<': '__lt__',
            "'": '__sq__',
            '"': '__dq__',
            '[': '__ob__',
            ']': '__cb__',
            '{': '__oc__',
            '}': '__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