spirepy.cli
===========

.. py:module:: spirepy.cli


Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/spirepy/cli/download/index
   /autoapi/spirepy/cli/spire/index
   /autoapi/spirepy/cli/view/index


Functions
---------

.. autoapisummary::

   spirepy.cli.download
   spirepy.cli.view
   spirepy.cli.main


Package Contents
----------------

.. py:function:: download(item: Union[spirepy.study.Study, spirepy.sample.Sample], target: str, output: str)

   Dowload data from a SPIRE item.

   :param item: The item to be viewed (:class:`spirepy.sample.Sample` or :class:`spirepy.study.Study`).
   :type item: :class:`spirepy.sample.Sample` or :class:`spirepy.study.Study`

   :param target: What you want to view (metadata, antibiotic resistance annotations, manifest)
   :type target: str

   :param output: The output folder where the items will be downloaded.
   :type output: str


.. py:function:: view(item: Union[spirepy.study.Study, spirepy.sample.Sample], target: str)

   View a SPIRE item.

   :param item: The item to be viewed (:class:`spirepy.sample.Sample` or :class:`spirepy.study.Study`).
   :type item: :class:`spirepy.sample.Sample` or :class:`spirepy.study.Study`

   :param target: What you want to view (metadata, antibiotic resistance annotations, manifest)
   :type target: str


.. py:function:: main()