def convert_inputfiles(cls,
                           folder=None,
                           inputfile=None,
                           session=None,
                           lod_threshold=None,
                           qtls_file='qtls.csv',
                           matrix_file='qtls_matrix.csv',
                           map_file='map.csv'):
        """ Convert the input files present in the given folder or
        inputfile.
        This method creates the matrix representation of the QTLs
        results providing for each marker position the LOD value found
        for each trait as well as a representation of the genetic map
        used in the experiment.
        The genetic map should be cleared of any markers added by the
        QTL mapping software.

        :kwarg folder: the path to the folder containing the files to
            check. This folder may contain sub-folders.
        :kwarg inputfile: the path to the input file to use
        :kwarg session: the session identifier used to identify which
            session to process
        :kwarg lod_threshold: the LOD threshold to apply to determine if
            a QTL is significant or not
        :kwarg qtls_file: a csv file containing the list of all the
            significant QTLs found in the analysis.
            The matrix is of type:
               trait, linkage group, position, Marker, LOD other columns
        :kwarg matrix_file: a csv file containing a matrix representation
            of the QTL data. This matrix is of type:
               marker, linkage group, position, trait1 lod, trait2, lod
        :kwarg map_file: a csv file containing the genetic map used
            in this experiment. The map is of structure:
               marker, linkage group, position

        """
        if folder is None and inputfile is None:
            raise MQ2Exception('You must specify either a folder or an '
                               'input file')

        sessions = cls.get_session_identifiers(folder)
        if session is None:
            raise MQ2NoSessionException(
                'The MapQTL plugin requires a session identifier to '
                'identify the session to process.'
                'Sessions are: %s' % ','.join(sessions))
        elif str(session) not in sessions:
            raise MQ2NoSuchSessionException(
                'The MapQTL session provided (%s) could not be found in the '
                'dataset. '
                'Sessions are: %s' % (session, ','.join(sessions)))

        if folder is not None:
            if not os.path.isdir(folder):  # pragma: no cover
                raise MQ2Exception('The specified folder is actually '
                                   'not a folder')
            else:
                inputfiles = cls.get_files(folder, session_id=session)

        if inputfile is not None:  # pragma: no cover
            if os.path.isdir(inputfile):
                raise MQ2Exception('The specified input file is actually '
                                   'a folder')
            else:
                inputfiles = [inputfile]

        try:
            lod_threshold = float(lod_threshold)
        except ValueError:
            raise MQ2Exception('LOD threshold should be a number')

        inputfiles.sort()

        # QTL matrix and QTL files
        qtl_matrix = []
        qtls = []
        filename = None
        for filename in inputfiles:
            matrix = read_input_file(filename)
            headers = matrix[0]
            qtl_matrix = get_qtls_matrix(qtl_matrix, matrix, filename)
            qtls.extend(get_qtls_from_mapqtl_data(matrix, lod_threshold,
                        filename))
        # format QTLs and write down the selection
        headers[0] = 'Trait name'
        qtls.insert(0, headers)
        write_matrix(qtls_file, qtls)

        # Write down the QTL matrix
        del(qtl_matrix[0])
        # Reorganize a couple of columns
        qtl_matrix.insert(0, qtl_matrix[2])
        del(qtl_matrix[3])
        # write output
        qtl_matrix = list(zip(*qtl_matrix))
        write_matrix(matrix_file, qtl_matrix)

        # Map matrix
        map_matrix = get_map_matrix(inputfiles[0])
        write_matrix(map_file, map_matrix)
Convert the input files present in the given folder or
        inputfile.
        This method creates the matrix representation of the QTLs
        results providing for each marker position the LOD value found
        for each trait as well as a representation of the genetic map
        used in the experiment.
        The genetic map should be cleared of any markers added by the
        QTL mapping software.

        :kwarg folder: the path to the folder containing the files to
            check. This folder may contain sub-folders.
        :kwarg inputfile: the path to the input file to use
        :kwarg session: the session identifier used to identify which
            session to process
        :kwarg lod_threshold: the LOD threshold to apply to determine if
            a QTL is significant or not
        :kwarg qtls_file: a csv file containing the list of all the
            significant QTLs found in the analysis.
            The matrix is of type:
               trait, linkage group, position, Marker, LOD other columns
        :kwarg matrix_file: a csv file containing a matrix representation
            of the QTL data. This matrix is of type:
               marker, linkage group, position, trait1 lod, trait2, lod
        :kwarg map_file: a csv file containing the genetic map used
            in this experiment. The map is of structure:
               marker, linkage group, position