galaxyInputBamB = sys.argv[3] repB = sys.argv[4] galaxyOutMergedBam = sys.argv[5] genome = sys.argv[6] expType = sys.argv[7] anaId = sys.argv[8] # No longer command line parameters: scriptPath = os.path.split(os.path.abspath(sys.argv[0]))[0] galaxyPath = '/'.join(scriptPath.split('/')[:-2]) settingsFile = scriptPath + '/' + "settingsE3.txt" # 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
galaxyInputFile = sys.argv[1] galaxyOutBamEval = sys.argv[2] genome = sys.argv[3] expType = sys.argv[4] repNo = sys.argv[5] anaId = sys.argv[6] # No longer command line parameters: scriptPath = os.path.split( os.path.abspath( sys.argv[0] ) )[0] galaxyPath = '/'.join(scriptPath.split('/')[ :-2 ]) settingsFile = scriptPath + '/' + "settingsE3.txt" # 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: 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