class Inputs(define.Inputs): bam = define.input(name="Read sequence", required=True, list=True, description="Read sequence in BAM format") bai = define.input(name="BAM index files", required=False, description="According BAM index", list=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False) dbSNP = define.input(name="dbSNP", required=False) Alleles = define.input(name="Alleles", required=False) comp = define.input(name="comp", required=False, description='Comparison file in VCF format') #ref_sample_calls = define.input(name="Reference Sample Calls", required=False, description = 'VCF file with the truth callset for the reference sample') BQSR = define.input( name="BQSR", required=False, description= 'Input covariates table file for on-the-fly base quality score recalibration' )
class Inputs(define.Inputs): vcfs = define.input(description="Input VCFs", required=True, list=True) #snp = define.input(description="SNP VCF", required=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False)
class Inputs(define.Inputs): vcf = define.input(description="Input VCF", required=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False) mask = define.input(name="Mask", required=False, description='Input ROD mask')
class Inputs(define.Inputs): #annotation = define.input(name = "Annotation", required = True, description = "Reference sequence") #reads = define.input(name = "Aligned Reads", required = True, description = "Reference sequence") reads = define.input(name='Read Sequence', list=True, required=True, description="Read Sequence")
class Inputs(define.Inputs): bam = define.input(name="Read sequence", required=True, description="Read sequence in BAM format", list=True) # , alt_path='/extra' bai = define.input(name="BAM index files", required=False, description="According BAM index", list=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False)
class Inputs(define.Inputs): bam = define.input( name="Read sequence", list=True, required=True, description="Read sequence in BAM format") #, alt_path='/extra' bai = define.input(name="BAM index files", required=False, description="According BAM index", list=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False) BQSR = define.input( name="BQSR", required=False, description= 'Input covariates table file for on-the-fly base quality score recalibration' ) Samplefiles = define.input(name="Sample Files", list=True, required=False)
class Inputs(define.Inputs): inp = define.input(description="Input VCF", required=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False) concordance = define.input(name="Concordance", required=False) discordance = define.input(name="Discordance", required=False) keepIDs = define.input(name="Keep IDs", required=False)
class Inputs(define.Inputs): In_vcf = define.input(name="Input VCF file", description="Input VCF file", required=True, list=False) In_vcf_tbi = define.input("Input TBI file", description="Index file for VCF", required=False, list=False) Reference = define.input( name="Reference", description="Reference sequence in FASTA format.", required=False, list=False) resource_hapmap = define.input( name="-resource:hapmap(for SNP VQSR)", description= "Hapmap sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run).", required=False, list=False) resource_omni = define.input( name="-resource:ommi(for SNP VQSR)", description= "1000G Omni sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run).", required=False, list=False) resource_1000G = define.input( name="-resource:1000G(for SNP VQSR)", description= "1000G SNPs for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run).", required=False, list=False) resource_dbsnp = define.input( name="-resource:dbsnp(for SNP VQSR)", description= "DbSNP sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run).", required=False, list=False) resource_mills = define.input( name="-resource:mills(for InDel VQSR)", description= "Mills_and_1000G_gold_standard indels for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run).", required=False, list=False)
class Inputs(define.Inputs): bam = define.input(description="BAM File", required=True, list=True) bai = define.input(name="BAM index files", required=False, description="According BAM index", list=True) dedup_bam_intervals = define.input(description="Dedup BAM Intervals", list=True, required=True) exclude_intervals = define.input(name="Exclude Intervals", list=True, required=False) exome_bed = define.input(name="Genomic Intervals", list=True, required=False) Gatk_key = define.input(name="GATK key", required=False)
class Inputs(define.Inputs): #annotation = define.input(name = "Annotation", required = True, description = "Reference sequence") #reads = define.input(name = "Aligned Reads", required = True, description = "Reference sequence") reads = define.input(name='Input SAM or BAM file', required=True, description="Input SAM or BAM file.")
class Inputs(define.Inputs): reads = define.input(name = "FASTQ Reads", list = True,description="A single FASTQ file for single end or two files for paired end experiments", required=True) adapter = define.input(name = "Adapters" , description="Alist of adapters to clip in FASTA format")