def test_write(self, tmpdir): yaml_conf = tmpdir / "conf.yml" yaml_conf.write(r""" numThreads: 4 fastaFiles: [test1.fasta,test2.fasta] parseRules: identifierParseRule: ^>.*\|(.*)\|.*$ paramGroups: - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0 fixedModifications: [mod1] variableModifications: [mod2,mod3] maxMissedCleavages: 1 """) mqpar_out = tmpdir / "mqpar.xml" t = MQParam(TEMPLATE_PATH, yaml=str(yaml_conf)) t.write(str(mqpar_out)) test = ET.parse(str(mqpar_out)).getroot() assert test.find('numThreads').text == '4' assert test.find('fastaFiles')[1].find( 'identifierParseRule').text == '^>.*\\|(.*)\\|.*$' assert [ el.text for el in test.find('parameterGroups')[0].find( 'variableModifications') ] == ['mod2', 'mod3']
parser.add_argument('--version', '-v', help="""A version number. Raises exception if it doesn't match the MaxQuant version of the template. For usage in the Galaxy tool.""") # in case numThreads is a environment variable, otherwise it can be specified in the yaml file as well parser.add_argument('--num_threads', '-t', help="Number of threads to specify in mqpar.") args = parser.parse_args() # edit file names, working dir is unknown at the time of galaxy tool configfile creation if args.yaml: with open(args.yaml) as f: conf_dict = yaml.safe_load(f.read()) for n, pg in enumerate(conf_dict['paramGroups']): for num, fl in enumerate(pg['files']): if not fl.startswith('/'): conf_dict['paramGroups'][n]['files'][num] = os.path.join(os.getcwd(), fl) with open('yaml', 'w') as f: yaml.safe_dump(conf_dict, stream=f) args.yaml = 'yaml' kwargs = dict(yaml=args.yaml) if args.substitution_rx: kwargs['substitution_rx'] = args.substitution_rx mqparam = MQParam(args.template, args.exp_design, **kwargs) if args.version and mqparam.version != args.version: raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version)) mqparam.set_simple_param('numThreads', args.num_threads) mqparam.write(args.mqpar_out if args.mqpar_out else 'mqpar.xml')
from mqparam import MQParam parser = argparse.ArgumentParser() arguments = ('--infiles', '--version', '--num_threads', '--substitution_rx', '--fasta_files', '--description_parse_rule', '--identifier_parse_rule', 'mqpar') for arg in arguments: parser.add_argument(arg) args = parser.parse_args() mqpar_out = os.path.join(os.getcwd(), 'mqpar.xml') infiles = [os.path.join(os.getcwd(), f) for f in args.infiles.split(',')] mqparam = MQParam(args.mqpar, None, substitution_rx=args.substitution_rx) if mqparam.version != args.version: raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version)) mqparam.translate(infiles) mqparam.add_fasta_files(args.fasta_files.split(','), {'identifierParseRule': args.identifier_parse_rule, 'descriptionParseRule': args.description_parse_rule}) mqparam.set_simple_param('numThreads', args.num_threads) mqparam.write('mqpar.xml')