flag_helper = list(zip(flags, helps, codes))

            for flag, helper, codelist in flag_helper:
                parts = flag.split(' ')
                flag = parts[0]
                flag_params = None

                if len(parts) > 1:
                    flag_params = parts[1:]

                #flag, flag_params, short, help
                tmp_section.insertFlag(flag, flag_params, helper, codelist)


dd = Document2Section(sys.argv[1])

with open('iqtree.inputs.xml', 'w') as f:

    macros = doc.createElement('macros')
    xml_inp = doc.createElement('xml')
    xml_inp.setAttribute('name', 'inputs')

    xml_inp.appendChild(dd.inputs)
    macros.appendChild(xml_inp)

    print(macros.toprettyxml(), file=f)
    f.close()

CommandParse("iqtree", dd.inputs, exclude_map, "iqtree.command.xml")