def addWorkflowGroupOptions(self,group) :
group.add_option("--normalBam", type="string",dest="normalBam",metavar="FILE",
help="Normal sample BAM file. [required] (no default)")
group.add_option("--tumorBam", type="string",dest="tumorBam",metavar="FILE",
help="Tumor sample BAM file. [optional] (no default)")
# group.add_option("--aligner", type="string",dest="alignerMode",metavar="ALIGNER",
# help="Aligner type. Accepted option are {%s} [required] (no default)" % (",".join(['%s' % (x) for x in self.validAlignerModes])))
group.add_option("--exome", dest="isExome", action="store_true",
help="Turn off depth filters which don't make sense for exome or other targeted output.")
# TODO:
# need argument to set the workflow to either ISAAC or bwa mode
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self,group) :
group.add_option("--bam","--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append",
help="Normal sample BAM or CRAM file. May be specified more than once, multiple inputs will be treated as each BAM file representing a different sample. [optional] (no default)")
group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append",
help="Tumor sample BAM or CRAM file. Only up to one tumor bam file accepted. [optional] (no default)")
group.add_option("--exome", dest="isExome", action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option("--rna", dest="isRNA", action="store_true",
help="Set options for RNA-Seq input. Must specify exactly one bam input file")
group.add_option("--unstrandedRNA", dest="isUnstrandedRNA", action="store_true",
help="Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self,group) :
group.add_option("--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append",
help="Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)")
group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append",
help="Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)")
group.add_option("--exome", dest="isExome", action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option("--rna", dest="isRNA", action="store_true",
help="Set options for RNA-Seq input: turn off depth filters and don't treat "
"anomalous reads as SV evidence when the proper-pair bit is set.")
group.add_option("--unstrandedRNA", dest="isUnstrandedRNA", action="store_true",
help="Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self,group) :
group.add_option("--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append",
help="Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [at least one required] (no default)")
group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append",
help="Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)")
# group.add_option("--aligner", type="string",dest="alignerMode",metavar="ALIGNER",
# help="Aligner type. Accepted option are {%s} [required] (no default)" % (",".join(['%s' % (x) for x in self.validAlignerModes])))
group.add_option("--exome", dest="isExome", action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option("--rna", dest="isRNA", action="store_true",
help="Set options for RNA-Seq input: turn off depth filters and don't treat "
"anomalous reads as SV evidence when the proper-pair bit is set.")
group.add_option("--referenceFasta",type="string",dest="referenceFasta",metavar="FILE",
help="samtools-indexed reference fasta file [required] (default: %default)")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self, group):
group.add_option(
"--bam",
"--normalBam",
type="string",
dest="normalBamList",
metavar="FILE",
action="append",
help=
"Normal sample BAM or CRAM file. May be specified more than once, multiple inputs will be treated as each BAM file representing a different sample. [optional] (no default)"
)
group.add_option(
"--tumorBam",
"--tumourBam",
type="string",
dest="tumorBamList",
metavar="FILE",
action="append",
help=
"Tumor sample BAM or CRAM file. Only up to one tumor bam file accepted. [optional] (no default)"
)
group.add_option(
"--exome",
dest="isExome",
action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option(
"--rna",
dest="isRNA",
action="store_true",
help=
"Set options for RNA-Seq input. Must specify exactly one bam input file"
)
group.add_option(
"--unstrandedRNA",
dest="isUnstrandedRNA",
action="store_true",
help=
"Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand"
)
group.add_option("--outputContig",
dest="isOutputContig",
action="store_true",
help="Output assembled contig sequences in VCF file")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self, group)
def addWorkflowGroupOptions(self, group):
group.add_option(
"--normalBam",
type="string",
dest="normalBamList",
metavar="FILE",
action="append",
help=
"Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [at least one required] (no default)"
)
group.add_option(
"--tumorBam",
"--tumourBam",
type="string",
dest="tumorBamList",
metavar="FILE",
action="append",
help=
"Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)"
)
# group.add_option("--aligner", type="string",dest="alignerMode",metavar="ALIGNER",
# help="Aligner type. Accepted option are {%s} [required] (no default)" % (",".join(['%s' % (x) for x in self.validAlignerModes])))
group.add_option(
"--exome",
dest="isExome",
action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option(
"--rna",
dest="isRNA",
action="store_true",
help=
"Set options for RNA-Seq input: turn off depth filters and don't treat "
"anomalous reads as SV evidence when the proper-pair bit is set.")
group.add_option(
"--referenceFasta",
type="string",
dest="referenceFasta",
metavar="FILE",
help=
"samtools-indexed reference fasta file [required] (default: %default)"
)
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self, group)
