def main(): parser = argparse.ArgumentParser() parser.add_argument("tool", type=str) parser.add_argument("job_order", type=str) parser.add_argument("--conformance-test", action="store_true") args = parser.parse_args() print json.dumps(cli.gen_cli(from_url(args.tool), from_url(args.job_order)))
def run_tests(doc_path, tool_key='tool', test_key='tests'): doc = from_url(doc_path) tests = doc[test_key] for test in tests: tool = test.get(tool_key) if test_cmd_line(tool, test.get('test_job'), test): print 'Test %s completed successfully!' % test.get('id') else: print 'Test %s completed failed!' % test.get('id')
def test_tmap_mapall(): path = os.path.join(os.path.dirname(__file__), '../examples/tmap.yml') doc = from_url(path) tool, job = doc['mapall'], doc['exampleJob'] print(gen_cli(tool, job))
def test_bwa_mem(): path = os.path.join(os.path.dirname(__file__), '../examples/bwa-mem.yml') doc = from_url(path) tool, job = doc['tool'], doc['job'] print(gen_cli(tool, job))
def test_tmap_mapall(): path = os.path.join(os.path.dirname(__file__), "../examples/tmap.yml") doc = from_url(path) tool, job = doc["mapall"], doc["exampleJob"] print gen_cli(tool, job)
def test_bwa_mem(): path = os.path.join(os.path.dirname(__file__), "../examples/bwa-mem.yml") doc = from_url(path) tool, job = doc["tool"], doc["job"] print gen_cli(tool, job)
def cmd_line(doc_path, tool_key='tool', job_key='job'): doc = from_url(doc_path) tool, job = doc[tool_key], doc[job_key] return Adapter(tool).cmd_line(job)
def validate_all(): validate_schema(TOOL_SCHEMA) validate_schema(META_SCHEMA) validate_tool(from_url('../examples/bwa-mem.yml')['tool']) validate_tool(from_url('../examples/tmap.yml')['mapall'])