Generates a string containing the parameters for a pParse parameter file
    but doesn't write any file yet.

    :param rawfilepath: location of the thermo ".raw" file
    :param outputpath: path to the output directory of pParse
    :param isolationWindow: MSn isolation window that was used for the
        aquisition of the specified thermo raw file
    :param coElute: 0 or 1, see "[Advanced Options]" below

    :returns: string containing pParse parameters

    .. note:
        # pParse.para params template
        # For help: mail to tuhuijun@ict.ac.cn
        # Time: 2014.12.08

        [Basic Options]
        datapath = C:\filedirectory\filename
        logfilepath = C:\filedirectory
        outputpath = C:\filedirectory

        [Advanced Options]
        co-elute = 1
        # 0, output single precursor for single scan;
        # 1, output all co-eluted precursors.
        input_format = raw
        # raw / ms1
        isolation_width = 1.6
        # 2 / 2.5 / 3 / 4
        mars_threshold = -0.5
        ipv_file = .\IPV.txt
        trainingset = EmptyPath

        [Internal Switches]
        output_mars_y = 0
        delete_msn = 0
        output_mgf = 1
        output_pf = 1
        debug_mode = 0
        check_activationcenter = 1
        output_all_mars_y = 0
        rewrite_files = 0
        export_unchecked_mono = 0
        cut_similiar_mono = 1
        mars_model = 4
        output_trainingdata = 0

def generateParams(rawfilepath, outputpath, isolationWindow, coElute):
    """Generates a string containing the parameters for a pParse parameter file
    but doesn't write any file yet.

    :param rawfilepath: location of the thermo ".raw" file
    :param outputpath: path to the output directory of pParse
    :param isolationWindow: MSn isolation window that was used for the
        aquisition of the specified thermo raw file
    :param coElute: 0 or 1, see "[Advanced Options]" below

    :returns: string containing pParse parameters

    .. note:
        # pParse.para params template
        # For help: mail to tuhuijun@ict.ac.cn
        # Time: 2014.12.08

        [Basic Options]
        datapath = C:\filedirectory\filename
        logfilepath = C:\filedirectory
        outputpath = C:\filedirectory

        [Advanced Options]
        co-elute = 1
        # 0, output single precursor for single scan;
        # 1, output all co-eluted precursors.
        input_format = raw
        # raw / ms1
        isolation_width = 1.6
        # 2 / 2.5 / 3 / 4
        mars_threshold = -0.5
        ipv_file = .\IPV.txt
        trainingset = EmptyPath

        [Internal Switches]
        output_mars_y = 0
        delete_msn = 0
        output_mgf = 1
        output_pf = 1
        debug_mode = 0
        check_activationcenter = 1
        output_all_mars_y = 0
        rewrite_files = 0
        export_unchecked_mono = 0
        cut_similiar_mono = 1
        mars_model = 4
        output_trainingdata = 0
    """
    output = str()
    #Basic options
    output = '\n'.join([output, ' = '.join(['datapath', rawfilepath])])
    output = '\n'.join([output, ' = '.join(['logfilepath', outputpath])])
    output = '\n'.join([output, ' = '.join(['outputpath', outputpath])])
    #Advanced options
    output = '\n'.join([output, ' = '.join(['co-elute', str(coElute)])])
    output = '\n'.join([output, ' = '.join(['input_format', 'raw'])])
    output = '\n'.join([output, ' = '.join(['isolation_width',
                                            str(isolationWindow)]
                                            )])
    output = '\n'.join([output, ' = '.join(['mars_threshold', '-0.5'])])
    output = '\n'.join([output, ' = '.join(['ipv_file', '.\IPV.txt'])])
    output = '\n'.join([output, ' = '.join(['trainingset', 'EmptyPath'])])
    #Internal Switches
    output = '\n'.join([output, ' = '.join(['output_mars_y', '0'])])
    output = '\n'.join([output, ' = '.join(['delete_msn', '0'])])
    output = '\n'.join([output, ' = '.join(['output_mgf', '1'])])
    output = '\n'.join([output, ' = '.join(['output_pf', '0'])])
    output = '\n'.join([output, ' = '.join(['debug_mode', '0'])])
    output = '\n'.join([output, ' = '.join(['check_activationcenter', '1'])])
    output = '\n'.join([output, ' = '.join(['output_all_mars_y', '0'])])
    output = '\n'.join([output, ' = '.join(['rewrite_files', '0'])])
    output = '\n'.join([output, ' = '.join(['export_unchecked_mono', '0'])])
    output = '\n'.join([output, ' = '.join(['cut_similiar_mono', '1'])])
    output = '\n'.join([output, ' = '.join(['mars_model', '4'])])
    output = '\n'.join([output, ' = '.join(['output_trainingdata', '0'])])

    return output