def collect_args():
parser = argparse.ArgumentParser(
prog="cwl2wdl",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser._optionals.title = "Options"
parser.add_argument("FILE", type=str, help="CWL file.")
parser.add_argument("-f", "--format", type=str, default="wdl",
choices=["wdl", "ast"],
help="specify the output format")
parser.add_argument("--validate", action="store_true",
help="validate the resulting WDL code with PyWDL")
parser.add_argument("--version", action='version',
version=str(cwl2wdl.__version__))
return parser
def collect_args():
parser = argparse.ArgumentParser(
prog="cwl2wdl", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser._optionals.title = "Options"
parser.add_argument("FILE", type=str, help="CWL file.")
parser.add_argument("-f",
"--format",
type=str,
default="wdl",
choices=["wdl", "ast"],
help="specify the output format")
parser.add_argument("--validate",
action="store_true",
help="validate the resulting WDL code with PyWDL")
parser.add_argument("--version",
action='version',
version=str(cwl2wdl.__version__))
return parser
def cli():
command_help = {
"run": "Run you a WDL",
"parse": "Parse a WDL file, print parse tree",
"expr": "Expression testing"
}
parser = argparse.ArgumentParser(description='Workflow Description Language (WDL)')
parser.add_argument(
'--version', action='version', version=str(pkg_resources.get_distribution('wdl'))
)
parser.add_argument(
'--debug', required=False, action='store_true', help='Open the floodgates'
)
parser.add_argument(
'--no-color', default=False, required=False, action='store_true', help="Don't colorize output"
)
subparsers = parser.add_subparsers(help='WDL Actions', dest='action')
subparsers.required = True
commands = {}
commands['run'] = subparsers.add_parser(
'run', description=command_help['run'], help=command_help['run']
)
commands['run'].add_argument(
'wdl_file', help='Path to WDL File'
)
commands['run'].add_argument(
'--inputs', help='Path to JSON file to define inputs'
)
commands['run'].add_argument(
'--sge', action="store_true", help='Use SGE to execute tasks'
)
commands['parse'] = subparsers.add_parser(
'parse', description=command_help['parse'], help=command_help['parse']
)
commands['parse'].add_argument(
'wdl_file', help='Path to WDL File'
)
cli = parser.parse_args()
if cli.action == 'run':
sys.exit('Currently unsupported')
inputs = {}
run_service_name = "local"
if cli.sge:
run_service_name = "sge"
if cli.inputs:
with open(cli.inputs) as fp:
inputs = json.loads(fp.read())
try:
wdl.engine.run(cli.wdl_file, run_service_name, inputs)
except wdl.engine.MissingInputsException as error:
print("Your workflow cannot be run because it is missing some inputs!")
if cli.inputs:
print("Add the following keys to your {} file and try again:".format(cli.inputs))
else:
print("Use the template below to specify the inputs. Keep the keys as-is and change the values to match the type specified")
print("Then, pass this file in as the --inputs option:\n")
print(json.dumps(error.missing, indent=4))
if cli.action == 'parse':
with open(cli.wdl_file) as fp:
ast = wdl.parser.parse(fp.read(), os.path.basename(cli.wdl_file)).ast()
print(ast.dumps(indent=2))
def main():
parser = argparse.ArgumentParser(description='Convert WDL to Toil')
parser.add_argument('wdl_file',
help='a WDL workflow or a directory with WDL files')
parser.add_argument('secondary_file',
help='secondary data file (json or yml)')
parser.add_argument('--tsv',
help='file with sample names for the scatter function')
args = parser.parse_args()
wdl_file_path = os.path.abspath(args.wdl_file)
args.secondary_file = os.path.abspath(args.secondary_file)
w = wdltoil(wdl_file_path, args)
##############################################################################
# read secondary file; create dictionary to hold variables
if args.secondary_file.endswith('.json'):
w.dict_from_JSON(args.secondary_file)
elif args.secondary_file.endswith('.yml'):
w.dict_from_YML(args.secondary_file)
else:
print('Unsupported Secondary File Type. Please specify json or yml.')
##############################################################################
formatted_WDL = w.format_WDL_code(wdl_file_path)
w.create_definitions(formatted_WDL)
w.create_jobs(formatted_WDL)
module_section = w.write_modules(w.module_list)
fn_section = w.write_functions()
main_section = w.write_main()
job_section = w.write_jobs()
# print('\n\n')
# for each_task in w.tasks_dictionary:
# print(each_task)
# for each_section in w.tasks_dictionary[each_task]:
# print(' ' + str(each_section))
# for each_variable in w.tasks_dictionary[each_task][each_section]:
# print(' ' + str(each_variable))
#
# print('\n\n')
# for each_task in w.jobs_dictionary:
# print(each_task)
# if 'wf_declarations' in w.jobs_dictionary[each_task]:
# print(' wf_declarations')
# for d in w.jobs_dictionary[each_task]['wf_declarations']:
# print(' ' + str(d))
# if 'job_declarations' in w.jobs_dictionary[each_task]:
# print(' job_declarations')
# for j in w.jobs_dictionary[each_task]['job_declarations']:
# print(' ' + str(j))
# for g in w.jobs_dictionary[each_task]['job_declarations'][j]:
# print(' ' + g + ': ' + w.jobs_dictionary[each_task]['job_declarations'][j][g])
#
# print('\n\n')
# for each_task in w.saved_scatter_input_vars:
# print(each_task)
# print(w.saved_scatter_input_vars[each_task])
w.write_python_file(module_section, fn_section, main_section, job_section,
w.output_file)
subprocess.check_call(['python', w.output_file])
