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())
# if tansformed/transformable bam is provided.
if alignedBy != 'unknown':
suffix = alignedBy.capitalize() + suffix
# What step expects:
# Inputs: 1 Annotation alignment bam keyed: 'annotation' + suffix + '.bam'
# Outputs: 1 target Gene results tab file, keyed: 'quantifyGenesRsem' + suffix + '.tab'
# 1 target Transcript results tab file, keyed: 'quantifyTranscriptsRsem' + suffix + '.tab'
bamInputKey = 'annotation' + suffix + '.bam' # Used to tie inputs together
genesFileKey = 'quantifyGenesRsem' + suffix + '.tab' # Used to tie outputs together
transFileKey = 'quantifyTranscriptsRsem' + suffix + '.tab'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamInputKey, 'galaxyInput', galaxyBamInput)
nonGalaxyInput = ana.nonGalaxyInput(
bamInputKey) # Registers and returns the outside location
# outputs:
ana.registerFile(genesFileKey, 'galaxyOutput', galaxyOutGenes)
resultsDir = ana.resultsDir(
galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(genesFileKey, 'nonGalaxyOutput', '%s_rsemGenes', ext='tab')
ana.registerFile(transFileKey, 'galaxyOutput', galaxyOutTrans)
ana.createOutFile(transFileKey,
'nonGalaxyOutput',
'%s_rsemTranscripts',
ext='tab')
# Establish step and run it:
step = RsemStep(ana, suffix)
sys.exit(step.run())
if testOnly:
ana.dryRun = testOnly
# What step expects:
# Inputs: 1 bam, pre-registered in the analysis keyed as: 'alignmentRep' + replicate + '.bam'
# 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')
# 'signalStarRep' + replicate + 'AllMinus.bw'
# 'signalStarRep' + replicate + 'AllPlus.bw'
# or 2 (unpaired) target signal file2: 'signalStarRep' + replicate + 'Uniq.bw'
# 'signalStarRep' + replicate + 'All.bw'
genoBamKey = 'genomeAlignedStarRep'+repNo + '.bam' # Used to tie outputs together
annoBamKey = 'annotationAlignedStarRep'+repNo + '.bam' # Used to tie outputs together
statsKey = 'statisticsStarRep'+repNo + '.txt' # Used to tie outputs together
# Establish Inputs for galaxy and nonGalaxy alike
if pairedOrUnpaired == "paired":
fastqRd1Key='tagsRd1Rep'+repNo + '.fastq' # Used to tie inputs together
fastqRd2Key='tagsRd2Rep'+repNo + '.fastq' # Used to tie inputs together
ana.registerFile(fastqRd1Key,'galaxyInput', galaxyInputFile)
ana.registerFile(fastqRd2Key,'galaxyInput', galaxyInputFile2)
nonGalaxyInput = ana.nonGalaxyInput(fastqRd1Key) # Registers and returns the outside location
nonGalaxyInput2 = ana.nonGalaxyInput(fastqRd2Key) # Registers and returns the outside location
# outputs:
ana.registerFile(genoBamKey,'galaxyOutput',galaxyGenoBamOutput)
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(genoBamKey,'nonGalaxyOutput','%s_%s_starGenome', ext='bam', \
input1=fastqRd1Key, input2=fastqRd2Key)
ana.registerFile(annoBamKey,'galaxyOutput',galaxyAnnoBamOutput)
ana.createOutFile(annoBamKey,'nonGalaxyOutput','%s_%s_starAnnotation', ext='bam', \
input1=fastqRd1Key, input2=fastqRd2Key)
ana.registerFile( statsKey, 'galaxyOutput',galaxyStatsOut)
ana.createOutFile(statsKey,'nonGalaxyOutput','%s_%s_starStats', ext='txt', \
input1=fastqRd1Key, input2=fastqRd2Key)
# signal bigWigs:
allMinusKey = 'signalStarRep' + repNo + 'AllMinus.bw'
ana.registerFile( allMinusKey, 'galaxyOutput',galaxyBwAllMinusOut)