if testOnly:
ana.dryRun = testOnly
# What step expects:
# Inputs: 2 bam files, pre-registered in the analysis and both keyed as: 'bamRep' + replicateN + '.bam'
# Outputs: 1 merged bam keyed as: 'mergedRep' + replicate1 + 'Rep' +replcicate2 + '.bam'
# set up keys that join inputs through various file forwardings:
bamAkey = 'bamRep' + repA + '.bam'
bamBkey = 'bamRep' + repB + '.bam'
mergedBamKey = 'mergedRep' + repA + 'Rep' + repB + '.bam'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamAkey, 'galaxyInput', galaxyInputBamA)
ana.registerFile(bamBkey, 'galaxyInput', galaxyInputBamB)
nonGalaxyInput1 = ana.nonGalaxyInput(
bamAkey) # Registers and returns the outside location
nonGalaxyInput2 = ana.nonGalaxyInput(
bamBkey) # Need to register these to ensure nonGalOut naming
# outputs:
ana.registerFile(mergedBamKey, 'galaxyOutput', galaxyOutMergedBam)
resultsDir = ana.resultsDir(
galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(mergedBamKey,'nonGalaxyOutput','%s_%s_merged',ext='bam', \
input1=bamAkey, input2=bamBkey)
# Establish step and run it:
step = MergeBamStep(ana, repA, repB)
sys.exit(step.run())
# Outputs: 1 interim Corr file, keyed as: 'strandCorr' + suffix + '.txt'
# 1 target json file, keyed as: 'bamEvaluate' + suffix + '.json'
# TODO: Does a galaxy user really want the sample bam?
# set up keys that join inputs through various file forwardings:
bamInputKey = 'alignmentRep' + repNo + '.bam'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamInputKey,'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(bamInputKey) # Registers and returns the outside location
suffix = 'Rep' + repNo
if nonGalaxyInput.lower().find('_star') != -1:
suffix += 'ByStar'
elif nonGalaxyInput.find('_tophat') != -1:
suffix += 'ByTophat'
elif nonGalaxyInput.lower().find('_bwa') != -1:
suffix += 'ByBwa'
bamSampleKey = 'alignment' + suffix + '_5M.bam'
bamEvalKey = 'bamEvaluate' + suffix + '.json'
# outputs:
ana.registerFile( bamEvalKey, 'galaxyOutput',galaxyOutBamEval)
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(bamEvalKey, 'nonGalaxyOutput','%s_bamEval',ext='json')
# Establish step and run it:
step = BamEvaluateStep(ana,repNo,suffix)
sys.exit( step.run() )
