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")
