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.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") 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 = 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)