def PhyDMSTestdivpressureParser():
    """Returns *argparse.ArgumentParser* for ``phdyms_testdivpressure``
        script.
    """
    parser = ArgumentParserNoArgHelp(description="Test different models of "
            "diversifying pressure. {0} Version {1}. Full documentation at {2}"\
            .format(phydmslib.__acknowledgments__, phydmslib.__version__,\
            phydmslib.__url__), formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument('outprefix', help='Prefix for output files.', type=str)
    parser.add_argument('alignment', help='Existing FASTA file with aligned '
            'codon sequences.', type=ExistingFile)
    parser.add_argument('prefsfile', help='Existing file with site-specific'
            ' amino-acid preferences.', type=ExistingFile)
    parser.add_argument('divpressure', help='List of existing files with '
            'diversifying pressure at each site', type=ExistingFile, nargs='+')
    group = parser.add_mutually_exclusive_group()
    group.add_argument('--tree', default=False, type=ExistingFile,
             help="Existing Newick file giving input tree.")
    group.add_argument('--raxml', help="Path to RAxML (http://sco.h-its.org/"
            "exelixis/software.html).", default='raxml')
    parser.add_argument('--randomizations', help = 'Number diversifying '
            'pressure randomizations.', default=0, type=NonNegativeInt)
    parser.add_argument('--ncpus', default=-1, help='Use this many CPUs; '
            '-1 means all available.', type=int)
    parser.add_argument('-v', '--version', action='version', version='%(prog)s '
            '{version}'.format(version=phydmslib.__version__))
    return parser
def PhyDMSTestdivpressureParser ( ) : parser = ArgumentParserNoArgHelp ( description = "Test different models of " "diversifying pressure. {0} Version {1}. Full documentation at {2}" . format ( phydmslib . __acknowledgments__ , phydmslib . __version__ , phydmslib . __url__ ) , formatter_class = argparse . ArgumentDefaultsHelpFormatter ) parser . add_argument ( 'outprefix' , help = 'Prefix for output files.' , type = str ) parser . add_argument ( 'alignment' , help = 'Existing FASTA file with aligned ' 'codon sequences.' , type = ExistingFile ) parser . add_argument ( 'prefsfile' , help = 'Existing file with site-specific' ' amino-acid preferences.' , type = ExistingFile ) parser . add_argument ( 'divpressure' , help = 'List of existing files with ' 'diversifying pressure at each site' , type = ExistingFile , nargs = '+' ) group = parser . add_mutually_exclusive_group ( ) group . add_argument ( '--tree' , default = False , type = ExistingFile , help = "Existing Newick file giving input tree." ) group . add_argument ( '--raxml' , help = "Path to RAxML (http://sco.h-its.org/" "exelixis/software.html)." , default = 'raxml' ) parser . add_argument ( '--randomizations' , help = 'Number diversifying ' 'pressure randomizations.' , default = 0 , type = NonNegativeInt ) parser . add_argument ( '--ncpus' , default = - 1 , help = 'Use this many CPUs; ' '-1 means all available.' , type = int ) parser . add_argument ( '-v' , '--version' , action = 'version' , version = '%(prog)s ' '{version}' . format ( version = phydmslib . __version__ ) ) return parser
Returns *argparse.ArgumentParser* for ``phdyms_testdivpressure``
        script.