How to use the planemo.io.write_file function in planemo

io.write_file(output, tool_description.contents)
    io.info("Tool written to %s" % output)
    for tool_file in tool_description.tool_files:
        if tool_file.contents is None:
            continue

        path = tool_file.filename
        if not io.can_write_to_path(path, **kwds):
            ctx.exit(1)
        io.write_file(path, tool_file.contents)
        io.info("Tool %s written to %s" % (tool_file.description, path))

    macros = kwds["macros"]
    macros_file = "macros.xml"
    if macros and not os.path.exists(macros_file):
        io.write_file(macros_file, tool_description.macro_contents)
    elif macros:
        io.info(REUSING_MACROS_MESSAGE)
    if tool_description.test_files:
        if not os.path.exists("test-data"):
            io.info("No test-data directory, creating one.")
            os.makedirs('test-data')
        for test_file in tool_description.test_files:
            io.info("Copying test-file %s" % test_file)
            try:
                shutil.copy(test_file, 'test-data')
            except Exception as e:
                io.info("Copy of %s failed: %s" % (test_file, e))

if not output:
        extension = "cwl" if kwds.get("cwl") else "xml"
        output = "%s.%s" % (tool_id, extension)
    if not io.can_write_to_path(output, **kwds):
        ctx.exit(1)

    io.write_file(output, tool_description.contents)
    io.info("Tool written to %s" % output)
    for tool_file in tool_description.tool_files:
        if tool_file.contents is None:
            continue

        path = tool_file.filename
        if not io.can_write_to_path(path, **kwds):
            ctx.exit(1)
        io.write_file(path, tool_file.contents)
        io.info("Tool %s written to %s" % (tool_file.description, path))

    macros = kwds["macros"]
    macros_file = "macros.xml"
    if macros and not os.path.exists(macros_file):
        io.write_file(macros_file, tool_description.macro_contents)
    elif macros:
        io.info(REUSING_MACROS_MESSAGE)
    if tool_description.test_files:
        if not os.path.exists("test-data"):
            io.info("No test-data directory, creating one.")
            os.makedirs('test-data')
        for test_file in tool_description.test_files:
            io.info("Copying test-file %s" % test_file)
            try:
                shutil.copy(test_file, 'test-data')

docker_enable = str(kwds.get("docker", False))
        docker_host = str(kwds.get("docker_host", docker_util.DEFAULT_HOST))
        docker_host_param = ""
        if docker_host:
            docker_host_param = """%s""" % docker_host

        conf_contents = Template(template_str).safe_substitute({
            "server_name": server_name,
            "docker_enable": docker_enable,
            "require_container": "false",
            "docker_sudo": str(kwds.get("docker_sudo", False)),
            "docker_sudo_cmd": str(kwds.get("docker_sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND)),
            "docker_cmd": str(kwds.get("docker_cmd", docker_util.DEFAULT_DOCKER_COMMAND)),
            "docker_host": docker_host_param,
        })
        write_file(job_config_file, conf_contents)
    kwds["job_config_file"] = job_config_file

enable_beta_tool_formats="True",
            id_secret="${id_secret}",
            log_level="${log_level}",
            debug="${debug}",
            watch_tools="auto",
            default_job_shell="/bin/bash",  # For conda dependency resolution
            tool_data_table_config_path=tool_data_table,
            data_manager_config_file=",".join(data_manager_config_paths) or None,  # without 'or None' may raise IOError in galaxy (see #946)
            integrated_tool_panel_config=("${temp_directory}/"
                                          "integrated_tool_panel_conf.xml"),
            migrated_tools_config=empty_tool_conf,
            test_data_dir=test_data_dir,  # TODO: make gx respect this
            shed_data_manager_config_file=shed_data_manager_config_file,
        ))
        _handle_container_resolution(ctx, kwds, properties)
        write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args))
        if not for_tests:
            properties["database_connection"] = _database_connection(database_location, **kwds)

        _handle_kwd_overrides(properties, kwds)

        # TODO: consider following property
        # watch_tool = False
        # datatypes_config_file = config/datatypes_conf.xml
        # welcome_url = /static/welcome.html
        # logo_url = /
        # sanitize_all_html = True
        # serve_xss_vulnerable_mimetypes = False
        # track_jobs_in_database = None
        # outputs_to_working_directory = False
        # retry_job_output_collection = 0

def _write_tool_conf(ctx, tool_paths, tool_conf_path):
    tool_definition = _tool_conf_entry_for(tool_paths)
    tool_conf_template_kwds = dict(tool_definition=tool_definition)
    tool_conf_contents = _sub(TOOL_CONF_TEMPLATE, tool_conf_template_kwds)
    write_file(tool_conf_path, tool_conf_contents)
    ctx.vlog(
        "Writing tool_conf to path %s with contents [%s]",
        tool_conf_path,
        tool_conf_contents,
    )

def _configure_sheds_config_file(ctx, config_directory, **kwds):
    if "shed_target" not in kwds:
        kwds = kwds.copy()
        kwds["shed_target"] = "toolshed"
    shed_target_url = tool_shed_url(ctx, **kwds)
    contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url})
    tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml")
    write_file(tool_sheds_conf, contents)
    return tool_sheds_conf