transform a allPeptides.txt and experimentalDesign.txt table
    into the dependentPeptides.txt table written in outfile.
    :param paramfile: Perseus parameters.xml including at least two FileParam
    entries names 'allPeptides.txt' and 'experimentalDesign.txt'.
    :param outfile: Path to the output file.

def run_dependent_peptides_from_parameters(paramfile, outfile):
    """ transform a allPeptides.txt and experimentalDesign.txt table
    into the dependentPeptides.txt table written in outfile.
    :param paramfile: Perseus parameters.xml including at least two FileParam
    entries names 'allPeptides.txt' and 'experimentalDesign.txt'.
    :param outfile: Path to the output file.
    """
    parameters = parse_parameters(paramfile)
    allPeptides_file = fileParam(parameters, 'allPeptides.txt')
    rawFilesTable_file = fileParam(parameters, 'Raw files table')
    run_dependent_peptides(allPeptides_file, rawFilesTable_file, outfile)