isPaired = valJson['isPaired']
tagLength = int(valJson['readSizeMean'])
#tagLength = (valJson['readSizeMax'] + valJson['readSizeMin']) / 2
except:
pass # TODO: Require this?
# TODO: suffix needs to know whether this is being run on a sample!
suffix = "Rep" + repNo
if fullOrSample == 'sample':
suffix = suffix + '_sample'
# Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended
ana = GalaxyAnalysis(settingsFile, anaId, genome, expType)
if testOnly:
ana.dryRun = testOnly
ana.setVar('tagLen', tagLength)
# What step expects:
# Inputs: 1 bam, pre-registered in analysis keyed as: 'alignment' + suffix + '.bam'
# Outputs: target broadPeak hotspot file, keyed as: 'hot' + suffix + '.bigBed'
# target narrowPeak peaks file, keyed as: 'peaks' + suffix + '.bigBed'
# target density bigWig file, keyed as: 'density' + suffix + '.bigWig'
# set up keys that join inputs through various file forwardings:
bamInputKey = 'alignment' + suffix + '.bam'
hotKey = 'hot' + suffix + '.bigBed'
peakKey = 'peaks' + suffix + '.bigBed'
densityKey = 'density' + suffix + '.bigWig'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamInputKey, 'galaxyInput', galaxyInputFile)
isPaired = valJson['isPaired']
tagLength = int(valJson['readSizeMean'])
#tagLength = (valJson['readSizeMax'] + valJson['readSizeMin']) / 2
except:
pass # TODO: Require this?
# TODO: suffix needs to know whether this is being run on a sample!
suffix = "Rep" + repNo
if fullOrSample == 'sample':
suffix = suffix + '_sample'
# Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended
ana = GalaxyAnalysis(settingsFile, anaId, genome, expType)
if testOnly:
ana.dryRun = testOnly
ana.setVar('tagLen',tagLength)
# What step expects:
# Inputs: 1 bam, pre-registered in analysis keyed as: 'alignment' + suffix + '.bam'
# Outputs: target broadPeak hotspot file, keyed as: 'hot' + suffix + '.bigBed'
# target narrowPeak peaks file, keyed as: 'peaks' + suffix + '.bigBed'
# target density bigWig file, keyed as: 'density' + suffix + '.bigWig'
# set up keys that join inputs through various file forwardings:
bamInputKey = 'alignment' + suffix + '.bam'
hotKey = 'hot' + suffix + '.bigBed'
peakKey = 'peaks' + suffix + '.bigBed'
densityKey = 'density' + suffix + '.bigWig'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamInputKey,'galaxyInput', galaxyInputFile)
