How to use the planemo.shed2tap.base.BaseAction function in planemo

def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupRubyEnvironmentAction(BaseAction):
    action_type = "setup_ruby_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupPythonEnvironmentAction(BaseAction):
    action_type = "setup_python_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupVirtualenvAction(BaseAction):
    action_type = "setup_virtualenv"
    _keys = ["use_requirements_file", "python", "requirements"]

    def __init__(self, elem):
        use_reqs = elem.attrib.get("use_requirements_file", "True")
        self.use_requirements_file = asbool(use_reqs)
        self.python = elem.get('python', 'python')

def to_bash(self):
        return ["chmod %s %s" % (m["mode"], m["target"]) for m in self.mods], []


class MakeInstallAction(BaseAction):
    action_type = "make_install"
    _keys = []

    def __init__(self, elem):
        pass

    def to_bash(self):
        return ["make install"], []


class AutoconfAction(BaseAction):
    action_type = "autoconf"
    _keys = ["options"]

    def __init__(self, elem):
        self.options = elem.text

    def to_bash(self):
        if self.options:
            raise NotImplementedError("Options with action autoconf not implemented yet.")
        return ['./configure', 'make', 'make install'], []


class ChangeDirectoryAction(BaseAction):
    action_type = "change_directory"
    _keys = ["directory"]

mods = []
        file_els = elem.findall("file")
        assert file_els is not None
        for mod_elem in file_els:
            mod = {}
            mod["mode"] = mod_elem.attrib["mode"]
            mod["target"] = mod_elem.text
            mods.append(mod)
        self.mods = mods
        assert self.mods

    def to_bash(self):
        return ["chmod %s %s" % (m["mode"], m["target"]) for m in self.mods], []


class MakeInstallAction(BaseAction):
    action_type = "make_install"
    _keys = []

    def __init__(self, elem):
        pass

    def to_bash(self):
        return ["make install"], []


class AutoconfAction(BaseAction):
    action_type = "autoconf"
    _keys = ["options"]

    def __init__(self, elem):
        self.options = elem.text

self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupVirtualenvAction(BaseAction):
    action_type = "setup_virtualenv"
    _keys = ["use_requirements_file", "python", "requirements"]

    def __init__(self, elem):
        use_reqs = elem.attrib.get("use_requirements_file", "True")
        self.use_requirements_file = asbool(use_reqs)
        self.python = elem.get('python', 'python')
        self.requirements = elem.text or 'requirements.txt'


class SetupREnvironmentAction(BaseAction):
    action_type = "setup_r_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetEnvironmentForInstallAction(BaseAction):
    action_type = "set_environment_for_install"

    def __init__(self, elem):
        pass

    def to_bash(self):
        # TODO - How could we resolve/check the dependencies?

def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupPythonEnvironmentAction(BaseAction):
    action_type = "setup_python_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupVirtualenvAction(BaseAction):
    action_type = "setup_virtualenv"
    _keys = ["use_requirements_file", "python", "requirements"]

    def __init__(self, elem):
        use_reqs = elem.attrib.get("use_requirements_file", "True")
        self.use_requirements_file = asbool(use_reqs)
        self.python = elem.get('python', 'python')
        self.requirements = elem.text or 'requirements.txt'


class SetupREnvironmentAction(BaseAction):
    action_type = "setup_r_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)

def to_bash(self):
        answer = []
        for var in self.variables:
            # Expand $INSTALL_DIR here?
            if var.action == "set_to":
                answer.append('export %s=%s' % (var.name, var.raw_value))
            elif var.action == "prepend_to":
                answer.append('export %s=%s:$%s' % (var.name, var.raw_value, var.name))
            elif var.action == "append_to":
                answer.append('export %s=$%s:%s' % (var.name, var.name, var.raw_value))
            else:
                raise ValueError("Undefined environment variable action %r" % var.action)
        return answer, answer  # Actions needed in env.sh here!


class ChmodAction(BaseAction):
    action_type = "chmod"
    _keys = ["mods"]

    def __init__(self, elem):
        mods = []
        file_els = elem.findall("file")
        assert file_els is not None
        for mod_elem in file_els:
            mod = {}
            mod["mode"] = mod_elem.attrib["mode"]
            mod["target"] = mod_elem.text
            mods.append(mod)
        self.mods = mods
        assert self.mods

    def to_bash(self):

# This is inserted into the if-else for a fresh download only.
        # Note double space between checksum and filename:
        answer.append('    echo "%s  %s" | shasum -a 256 -c -' % (sha256sum, target_filename))
    answer.append('fi')

    return answer, downloaded_filename


def _commands_to_download_and_extract(url, target_filename=None, sha256sum=None):
    answer, downloaded_filename = _commands_and_downloaded_file(url, target_filename, sha256sum)
    # Now should we unpack the tar-ball etc?
    answer.extend(_determine_compressed_file_folder(url, downloaded_filename, target_filename, sha256sum))
    return answer, []


class DownloadByUrlAction(BaseAction):
    action_type = "download_by_url"
    _keys = ["url"]

    def __init__(self, elem):
        self.url = elem.text.strip()
        assert self.url
        self.sha256sum = elem.attrib.get("sha256sum", None)
        self.target_filename = elem.attrib.get("target_filename", None)

    def to_bash(self):
        # See class DownloadByUrl in Galaxy,
        # lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
        return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)


class DownloadFileAction(BaseAction):

action_type = "download_by_url"
    _keys = ["url"]

    def __init__(self, elem):
        self.url = elem.text.strip()
        assert self.url
        self.sha256sum = elem.attrib.get("sha256sum", None)
        self.target_filename = elem.attrib.get("target_filename", None)

    def to_bash(self):
        # See class DownloadByUrl in Galaxy,
        # lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
        return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)


class DownloadFileAction(BaseAction):
    action_type = "download_file"
    _keys = ["url", "extract"]

    def __init__(self, elem):
        self.url = elem.text.strip()
        self.extract = asbool(elem.attrib.get("extract", False))
        self.sha256sum = elem.attrib.get("sha256sum", None)
        self.target_filename = elem.attrib.get("target_filename", None)

    def to_bash(self):
        if self.extract:
            return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)
        else:
            commands, downloaded_file = _commands_and_downloaded_file(self.url, self.target_filename, self.sha256sum)
            return commands, []

def parse_action(self, action):
        return BaseAction.from_elem(action, package=self)

def to_bash(self):
        return ["cd %s" % self.directory], []


class MakeDirectoryAction(BaseAction):
    action_type = "make_directory"
    _keys = ["directory"]

    def __init__(self, elem):
        self.directory = elem.text

    def to_bash(self):
        return ["mkdir -p %s" % self.directory], []


class SetupPerlEnvironmentAction(BaseAction):
    action_type = "setup_perl_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)


class SetupRubyEnvironmentAction(BaseAction):
    action_type = "setup_ruby_environment"
    _keys = ["repo", "packages"]

    def __init__(self, elem):
        self.parse_action_repo(elem)
        self.parse_package_elems(elem)