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')
