Mercurial > repos > iuc > jbrowse
comparison jbrowse.py @ 16:b5c5470d7c09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
author | iuc |
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date | Wed, 13 Sep 2017 13:07:20 -0400 |
parents | 18be2d72fdee |
children | ff11d442feed |
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15:4e11a688a635 | 16:b5c5470d7c09 |
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434 if blastOpts.get('index', 'false') == 'true': | 434 if blastOpts.get('index', 'false') == 'true': |
435 self.tracksToIndex.append("%s" % trackData['label']) | 435 self.tracksToIndex.append("%s" % trackData['label']) |
436 | 436 |
437 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): | 437 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
438 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | 438 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') |
439 cmd = ['ln', data, dest] | 439 cmd = ['ln', '-s', data, dest] |
440 self.subprocess_check_call(cmd) | 440 self.subprocess_check_call(cmd) |
441 | 441 |
442 url = os.path.join('raw', trackData['label'] + '.bw') | 442 url = os.path.join('raw', trackData['label'] + '.bw') |
443 trackData.update({ | 443 trackData.update({ |
444 "urlTemplate": url, | 444 "urlTemplate": url, |
564 'description': track['style'].get('description', ''), | 564 'description': track['style'].get('description', ''), |
565 }, | 565 }, |
566 'category': track['category'], | 566 'category': track['category'], |
567 } | 567 } |
568 | 568 |
569 mapped_chars = { | |
570 '>': '__gt__', | |
571 '<': '__lt__', | |
572 "'": '__sq__', | |
573 '"': '__dq__', | |
574 '[': '__ob__', | |
575 ']': '__cb__', | |
576 '{': '__oc__', | |
577 '}': '__cc__', | |
578 '@': '__at__', | |
579 '#': '__pd__' | |
580 } | |
581 | |
569 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']): | 582 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']): |
583 # Unsanitize labels (element_identifiers are always sanitized by Galaxy) | |
584 for key, value in mapped_chars.items(): | |
585 track_human_label = track_human_label.replace(value, key) | |
586 | |
570 log.info('Processing %s / %s', track['category'], track_human_label) | 587 log.info('Processing %s / %s', track['category'], track_human_label) |
571 outputTrackConfig['key'] = track_human_label | 588 outputTrackConfig['key'] = track_human_label |
572 hashData = [dataset_path, track_human_label, track['category']] | 589 hashData = [dataset_path, track_human_label, track['category']] |
573 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i | 590 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i |
574 | 591 |