.. cellorganizer_pipeline:

=====================
CellOrganizer Options
=====================
Options listed for the 5 main functions of CellOrganizer. Default setting shown in brackets (**[]**).

.. include:: cellorganizer_options/img2slml_options.rst

.. include:: cellorganizer_options/slml2img_options.rst

.. include:: cellorganizer_options/slml2info_options.rst

.. include:: cellorganizer_options/slml2report_options.rst

.. include:: cellorganizer_options/slml2slml_options.rst

.. include:: cellorganizer_options/options_for_galaxy.rst

.. include:: cellorganizer_options/options_for_docker.rst