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 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())
# 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() )
# 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)
nonGalaxyInput = ana.nonGalaxyInput(
bamInputKey) # Registers and returns the outside location
# outputs:
ana.registerFile(hotKey, 'galaxyOutput', galaxyOutputHot)
ana.registerFile(peakKey, 'galaxyOutput', galaxyOutputPeaks)
ana.registerFile(densityKey, 'galaxyOutput', galaxyOutputDensity)
resultsDir = ana.resultsDir(
galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(hotKey, 'nonGalaxyOutput', ext='bigBed')
ana.createOutFile(peakKey, 'nonGalaxyOutput', ext='bigBed')
ana.createOutFile(densityKey, 'nonGalaxyOutput', ext='bigWig')
# Establish step and run it:
step = HotspotStep(ana, suffix, tagLength)
sys.exit(step.run())
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)
ana.createOutFile(allMinusKey,'nonGalaxyOutput','%s_%s_starAllMinus', ext='bw', \
input1=fastqRd1Key, input2=fastqRd2Key)
allPlusKey = 'signalStarRep' + repNo + 'AllPlus.bw'
ana.registerFile( allPlusKey, 'galaxyOutput',galaxyBwAllPlusOut)
ana.createOutFile(allPlusKey,'nonGalaxyOutput','%s_%s_starAllPlus', ext='bw', \
input1=fastqRd1Key, input2=fastqRd2Key)
# What step expects:
# Inputs: 1 bam, pre-registered in analysis keyed as: 'alignment' + suffix + '.bam'
# 1 bam control (optional), pre-registered keyed as: 'control' + suffix + '.bam'
# Outputs: 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'
controlInputKey = 'control' + suffix + '.bam'
peakKey = 'peaks' + suffix + '.bigBed'
densityKey = 'density' + suffix + '.bigWig'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamInputKey,'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(bamInputKey) # Registers and returns the outside location
if expType.lower() == 'chipseq':
ana.registerFile(controlInputKey,'galaxyInput', galaxyInputFile)
ana.nonGalaxyInput(controlInputKey)
# outputs:
ana.registerFile( peakKey, 'galaxyOutput',galaxyOutputPeaks )
ana.registerFile( densityKey, 'galaxyOutput',galaxyOutputDensity)
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(peakKey, 'nonGalaxyOutput',ext='bigBed')
ana.createOutFile(densityKey, 'nonGalaxyOutput',ext='bigWig')
# Establish step and run it:
step = MacsStep(ana,suffix,expType,isPaired)
sys.exit( step.run() )
# Outputs: a single bam target keyed as:
# 'alignmentRep'+replicate+'.bam'
bamFileKey = 'alignmentRep'+repNo + '.bam' # Used to tie outputs togther
# Establish Inputs for galaxy and nonGalaxy alike
if pairedOrUnpaired == "paired":
fastqRd1Key='tagsRd1Rep'+repNo + '.fastq' # Used to tie inputs togther
fastqRd2Key='tagsRd2Rep'+repNo + '.fastq' # Used to tie inputs togther
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(bamFileKey,'galaxyOutput',galaxyOutputFile)
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(bamFileKey,'nonGalaxyOutput','%s_%s', ext='bam', \
input1=fastqRd1Key, input2=fastqRd2Key)
else:
fastqKey='tagsRep'+repNo + '.fastq' # Used to tie inputs togther
ana.registerFile(fastqKey,'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(fastqKey) # Registers and returns the outside location
# outputs:
ana.registerFile(bamFileKey,'galaxyOutput',galaxyOutputFile)
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(bamFileKey,'nonGalaxyOutput',ext='bam' )
# Establish step and run it:
step = BwaAlignmentStep(ana,repNo,encoding)
sys.exit( step.run() )
# 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
# 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 suffix == '-1':
suffix = ana.fileGetPart(galaxyInputFile, 'root')
inputKey = 'tags' + suffix + '.fastq'
valDirKey = 'fastqValDir' + suffix
valZipKey = 'fastqVal' + suffix + '.zip'
valHtmlKey = 'fastqVal' + suffix + '.html'
valJsonKey = 'fastqVal' + suffix + '.json'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(inputKey, 'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(
inputKey) # Registers and returns the outside location
# Output is complete dir
ana.registerFile(valDirKey, 'galaxyOutput', galaxyOutputDir)
ana.createOutFile(valDirKey, 'nonGalaxyOutput', '%s_sample_fastqc', ext='dir')
ana.createOutFile(valZipKey, 'nonGalaxyOutput', '%s_sample_fastqc', ext='zip')
ana.createOutFile(valJsonKey, 'nonGalaxyOutput', '%s_validate', ext='json')
# Galaxy needs to know about a single file within the dir. While it is moved to the analysisDir
# as part of the htmlDir, It must be manually moved for galaxy. Thus, the standard
# analysis file forwarding is slightly modified here:
ana.registerFile(valHtmlKey, 'galaxyOutput', galaxyOutputHtml)
nonGalaxyOutput = ana.createOutFile(valHtmlKey,'nonGalaxyOutput', \
'%s_sample_fastqc/fastqc_report', ext='html' )
#ana.registerFile(valZipKey,'galaxyOutput',galaxyOutputZip) # No need: galaxy zips it anyway
jsonOut = ana.registerFile(valJsonKey, 'galaxyOutput', galaxyOutSummary)
# This step needs closer control of how files are delivered:
ana.deliveryKeys([valDirKey, valZipKey,
valJsonKey]) # Restrict file delivery to just these
# Establish Inputs for galaxy and nonGalaxy alike
if pairedOrUnpaired == "paired":
fastqRd1Key = 'tagsRd1Rep' + repNo + '.fastq' # Used to tie inputs togther
fastqRd2Key = 'tagsRd2Rep' + repNo + '.fastq' # Used to tie inputs togther
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(bamFileKey, 'galaxyOutput', galaxyOutputFile)
resultsDir = ana.resultsDir(
galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(bamFileKey,'nonGalaxyOutput','%s_%s', ext='bam', \
input1=fastqRd1Key, input2=fastqRd2Key)
else:
fastqKey = 'tagsRep' + repNo + '.fastq' # Used to tie inputs togther
ana.registerFile(fastqKey, 'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(
fastqKey) # Registers and returns the outside location
# outputs:
ana.registerFile(bamFileKey, 'galaxyOutput', galaxyOutputFile)
resultsDir = ana.resultsDir(
galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(bamFileKey, 'nonGalaxyOutput', ext='bam')
# Establish step and run it:
step = BwaAlignmentStep(ana, repNo, encoding)
sys.exit(step.run())
suffix = ana.galaxyFileId(galaxyInputFile) # suffix needs to be based on the input file
if suffix == '-1':
suffix = ana.fileGetPart(galaxyInputFile,'root')
inputKey = 'tags' + suffix + '.fastq'
valDirKey = 'fastqValDir' + suffix
valZipKey = 'fastqVal' + suffix + '.zip'
valHtmlKey = 'fastqVal' + suffix + '.html'
valJsonKey = 'fastqVal' + suffix + '.json'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(inputKey,'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(inputKey) # Registers and returns the outside location
# Output is complete dir
ana.registerFile(valDirKey,'galaxyOutput',galaxyOutputDir)
ana.createOutFile(valDirKey,'nonGalaxyOutput', '%s_sample_fastqc', ext='dir' )
ana.createOutFile(valZipKey,'nonGalaxyOutput', '%s_sample_fastqc', ext='zip' )
ana.createOutFile(valJsonKey,'nonGalaxyOutput','%s_validate', ext='json' )
# Galaxy needs to know about a single file within the dir. While it is moved to the analysisDir
# as part of the htmlDir, It must be manually moved for galaxy. Thus, the standard
# analysis file forwarding is slightly modified here:
ana.registerFile(valHtmlKey,'galaxyOutput',galaxyOutputHtml)
nonGalaxyOutput = ana.createOutFile(valHtmlKey,'nonGalaxyOutput', \
'%s_sample_fastqc/fastqc_report', ext='html' )
#ana.registerFile(valZipKey,'galaxyOutput',galaxyOutputZip) # No need: galaxy zips it anyway
jsonOut = ana.registerFile(valJsonKey,'galaxyOutput',galaxyOutSummary)
# This step needs closer control of how files are delivered:
ana.deliveryKeys([valDirKey,valZipKey,valJsonKey]) # Restrict file delivery to just these
ana.deliverToGalaxyKeys([valDirKey,valZipKey,valHtmlKey,valJsonKey]) # Restrict delivery to these and in order
ana = GalaxyAnalysis(settingsFile, anaId, genome, expType)
if testOnly:
ana.dryRun = testOnly
suffix = "Rep" + repNo
if alignedBy != 'unknown':
suffix = alignedBy.capitalize() + suffix
# What step expects:
# Inputs: 1 bam, pre-registered in analysis, keyed as: 'alignment' + suffix + '.bam'
# Outputs: target signal file, keyed as: 'signal + suffix + readFiler + strand + '.bw'
# set up keys that join inputs through various file forwardings:
bamInputKey = 'alignment' + suffix + '.bam'
signalKey = 'signal' + suffix + readFilter + strand + '.bw'
# Establish Inputs for galaxy and nonGalaxy alike
ana.registerFile(bamInputKey,'galaxyInput', galaxyInputFile)
nonGalaxyInput = ana.nonGalaxyInput(bamInputKey) # Registers and returns the outside location
# outputs:
ana.registerFile( signalKey, 'galaxyOutput',galaxyOutSignal )
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(signalKey, 'nonGalaxyOutput', \
'%s_' + readFilter.lower() + strand.capitalize(),ext='bw')
# Establish step and run it:
step = BamToBwStep(ana,suffix,readFilter,strand)
sys.exit( step.run() )
# 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)
nonGalaxyInput = ana.nonGalaxyInput(bamInputKey) # Registers and returns the outside location
# outputs:
ana.registerFile( hotKey, 'galaxyOutput',galaxyOutputHot )
ana.registerFile( peakKey, 'galaxyOutput',galaxyOutputPeaks )
ana.registerFile( densityKey, 'galaxyOutput',galaxyOutputDensity)
resultsDir = ana.resultsDir(galaxyPath) # prefers nonGalaxyInput location over settings loc
ana.createOutFile(hotKey, 'nonGalaxyOutput',ext='bigBed')
ana.createOutFile(peakKey, 'nonGalaxyOutput',ext='bigBed')
ana.createOutFile(densityKey, 'nonGalaxyOutput',ext='bigWig')
# Establish step and run it:
step = HotspotStep(ana,suffix,tagLength)
sys.exit( step.run() )
# 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())
