"Modify a given mqpar.xml to run Galaxy MaxQuant with it."

import argparse
import os

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')