def test_translate(self): t = MQParam(TEMPLATE_PATH) t.add_infiles([('/posix/path/to/Test1.mzXML', '/posix/path/to/Test2.mzXML'), ('/path/dummy.mzXML',)]) # mqparam is not designed for windows t._root.find('filePaths')[2].text = r'D:\Windows\Path\Test3.mzXML' t.translate(('/galaxy/working/Test3.mzXML', '/galaxy/working/Test1.mzXML', '/galaxy/working/Test2.mzXML', '/galaxy/working/Test4.mzXML')) assert [e.text for e in t._root.find('filePaths')] == ['/galaxy/working/Test1.mzXML', '/galaxy/working/Test2.mzXML', '/galaxy/working/Test3.mzXML']
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')