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comparison jbrowse.py @ 13:69c5e9c0add0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
author iuc
date Thu, 09 Feb 2017 12:36:16 -0500
parents db5fe5a3176a
children 18be2d72fdee
comparison
equal deleted inserted replaced
12:db5fe5a3176a 13:69c5e9c0add0
422 '--clientConfig', json.dumps(clientConfig), 422 '--clientConfig', json.dumps(clientConfig),
423 '--config', json.dumps(config), 423 '--config', json.dumps(config),
424 '--trackType', 'JBrowse/View/Track/CanvasFeatures' 424 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
425 ] 425 ]
426 426
427 # className in --clientConfig is ignored, it needs to be set with --className
428 if 'className' in trackData['style']:
429 cmd += ['--className', trackData['style']['className']]
430
427 self.subprocess_check_call(cmd) 431 self.subprocess_check_call(cmd)
428 os.unlink(gff3) 432 os.unlink(gff3)
429 433
430 if blastOpts.get('index', 'false') == 'true': 434 if blastOpts.get('index', 'false') == 'true':
431 self.tracksToIndex.append("%s" % trackData['label']) 435 self.tracksToIndex.append("%s" % trackData['label'])
504 data, 508 data,
505 '--trackLabel', trackData['label'], 509 '--trackLabel', trackData['label'],
506 '--key', trackData['key'] 510 '--key', trackData['key']
507 ] 511 ]
508 512
513 # className in --clientConfig is ignored, it needs to be set with --className
514 if 'className' in trackData['style']:
515 cmd += ['--className', trackData['style']['className']]
516
509 config = copy.copy(trackData) 517 config = copy.copy(trackData)
510 clientConfig = trackData['style'] 518 clientConfig = trackData['style']
511 del config['style'] 519 del config['style']
512 520
513 if 'match' in gffOpts: 521 if 'match' in gffOpts:
526 config['transcriptType'] = gffOpts['transcriptType'] 534 config['transcriptType'] = gffOpts['transcriptType']
527 if 'subParts' in gffOpts and gffOpts['subParts']: 535 if 'subParts' in gffOpts and gffOpts['subParts']:
528 config['subParts'] = gffOpts['subParts'] 536 config['subParts'] = gffOpts['subParts']
529 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: 537 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
530 config['impliedUTRs'] = gffOpts['impliedUTRs'] 538 config['impliedUTRs'] = gffOpts['impliedUTRs']
539 elif trackType == 'JBrowse/View/Track/HTMLFeatures':
540 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
541 cmd += ['--type', gffOpts['transcriptType']]
531 542
532 cmd += [ 543 cmd += [
533 '--trackType', gffOpts['trackType'] 544 '--trackType', gffOpts['trackType']
534 ] 545 ]
535 546