.. _cli:

Command Line Interface
======================

Batchie provides a suite of command line utilities that allow users to script running the pipeline end to end.


.. _cli_train_model:

``train_model``
---------------

.. argparse::
   :ref: batchie.cli.train_model.get_parser
   :prog: train_model


.. _cli_evaluate_model:

``evaluate_model``
------------------

.. argparse::
   :ref: batchie.cli.evaluate_model.get_parser
   :prog: evaluate_model


.. _cli_calculate_distance_matrix:

``calculate_distance_matrix``
-----------------------------

.. argparse::
   :ref: batchie.cli.calculate_distance_matrix.get_parser
   :prog: calculate_distance_matrix


.. _cli_calculate_scores:

``calculate_scores``
---------------------

.. argparse::
   :ref: batchie.cli.calculate_scores.get_parser
   :prog: calculate_scores


.. _cli_select_next_plate:

``select_next_plate``
---------------------

.. argparse::
   :ref: batchie.cli.select_next_plate.get_parser
   :prog: select_next_plate


.. _cli_reveal_plate:

``reveal_plate``
----------------

.. argparse::
   :ref: batchie.cli.reveal_plate.get_parser
   :prog: reveal_plate


.. _cli_extract_screen_metadata:

``extract_screen_metadata``
---------------------------

.. argparse::
   :ref: batchie.cli.extract_screen_metadata.get_parser
   :prog: extract_screen_metadata


.. _cli_prepare_retrospective_simulation:

``prepare_retrospective_simulation``
------------------------------------

.. argparse::
   :ref: batchie.cli.prepare_retrospective_simulation.get_parser
   :prog: prepare_retrospective_simulation