def test_simple_param(self):
t = MQParam(TEMPLATE_PATH)
t.set_simple_param('minUniquePeptides', 4)
assert t._root.find('.minUniquePeptides').text == '4'
with pytest.raises(ValueError):
t.set_simple_param('foo', 3)
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')
