def parse_args(inputs):
parser = HelpArgParser(
description="Create a bcbio_sample.yaml file from a standard template and inputs")
parser.add_argument("template", help="Template name or path to template YAML file")
parser.add_argument("project_name", help="Name of the current project")
parser.add_argument("input_files", nargs="*", help="Input read files, in BAM or fastq format")
return parser.parse_args(inputs)
def parse_args(inputs):
parser = HelpArgParser(
description=
"Create a bcbio_sample.yaml file from a standard template and inputs")
parser.add_argument("template",
help="Template name or path to template YAML file")
parser.add_argument("project_name", help="Name of the current project")
parser.add_argument("input_files",
nargs="*",
help="Input read files, in BAM or fastq format")
return parser.parse_args(inputs)
def parse_args(inputs):
parser = HelpArgParser(
description="Create a bcbio_sample.yaml file from a standard template and inputs")
parser.add_argument("template", help=("Template name or path to template YAML file. "
"Built in choices: freebayes-variant, gatk-variant, tumor-paired, "
"noalign-variant, illumina-rnaseq, illumina-chipseq"))
parser.add_argument("metadata", help="CSV file with project metadata. Name of file used as project name.")
parser.add_argument("input_files", nargs="*", help="Input read files, in BAM or fastq format")
return parser.parse_args(inputs)
def parse_args(inputs):
parser = HelpArgParser(
description=
"Create a bcbio_sample.yaml file from a standard template and inputs")
parser.add_argument(
"template",
help=(
"Template name or path to template YAML file. "
"Built in choices: freebayes-variant, gatk-variant, tumor-paired, "
"noalign-variant, illumina-rnaseq, illumina-chipseq"))
parser.add_argument(
"metadata",
help=
"CSV file with project metadata. Name of file used as project name.")
parser.add_argument("input_files",
nargs="*",
help="Input read files, in BAM or fastq format")
return parser.parse_args(inputs)
def parse_args(inputs):
parser = HelpArgParser(
description="Create a bcbio_sample.yaml file from a standard template and inputs")
parser = setup_args(parser)
args = parser.parse_args(inputs)
if args.template.endswith("csv"):
parser.print_help()
print "\nError: Looks like you've swapped the order of the metadata CSV and template YAML arguments, it should go YAML first, CSV second."
sys.exit(1)
return parser.parse_args(inputs)
def parse_args(inputs):
parser = HelpArgParser(
description=
"Create a bcbio_sample.yaml file from a standard template and inputs")
parser = setup_args(parser)
return parser.parse_args(inputs)
def parse_args(inputs):
parser = HelpArgParser(
description="Create a bcbio_sample.yaml file from a standard template and inputs")
parser = setup_args(parser)
return parser.parse_args(inputs)
