========
Commands
========

Planemo is a set of utilities for developing Galaxy tools. Each utility is
implemented as a subcommand of the ``planemo`` executable. This section of the
documentation describes these commands.


.. include:: commands/autoupdate.rst
.. include:: commands/ci_find_repos.rst
.. include:: commands/ci_find_tools.rst
.. include:: commands/ci_setup.rst
.. include:: commands/cli_metadata.rst
.. include:: commands/clone.rst
.. include:: commands/conda_build.rst
.. include:: commands/conda_env.rst
.. include:: commands/conda_init.rst
.. include:: commands/conda_install.rst
.. include:: commands/conda_search.rst
.. include:: commands/config_init.rst
.. include:: commands/container_register.rst
.. include:: commands/create_alias.rst
.. include:: commands/database_create.rst
.. include:: commands/database_delete.rst
.. include:: commands/database_list.rst
.. include:: commands/delete_alias.rst
.. include:: commands/docker_build.rst
.. include:: commands/docker_shell.rst
.. include:: commands/dockstore_init.rst
.. include:: commands/docs.rst
.. include:: commands/format.rst
.. include:: commands/invocation_download.rst
.. include:: commands/invocation_export.rst
.. include:: commands/job_config_init.rst
.. include:: commands/lint.rst
.. include:: commands/list_alias.rst
.. include:: commands/list_invocations.rst
.. include:: commands/list_repos.rst
.. include:: commands/merge_test_reports.rst
.. include:: commands/mull.rst
.. include:: commands/mulled_init.rst
.. include:: commands/normalize.rst
.. include:: commands/open.rst
.. include:: commands/output_schema.rst
.. include:: commands/profile_create.rst
.. include:: commands/profile_delete.rst
.. include:: commands/profile_job_config_init.rst
.. include:: commands/profile_list.rst
.. include:: commands/project_init.rst
.. include:: commands/pull_request.rst
.. include:: commands/rerun.rst
.. include:: commands/run.rst
.. include:: commands/serve.rst
.. include:: commands/share_test.rst
.. include:: commands/shed_build.rst
.. include:: commands/shed_create.rst
.. include:: commands/shed_diff.rst
.. include:: commands/shed_init.rst
.. include:: commands/shed_lint.rst
.. include:: commands/shed_serve.rst
.. include:: commands/shed_test.rst
.. include:: commands/shed_update.rst
.. include:: commands/shed_upload.rst
.. include:: commands/slurm_init.rst
.. include:: commands/syntax.rst
.. include:: commands/test.rst
.. include:: commands/test_reports.rst
.. include:: commands/tool_init.rst
.. include:: commands/training_fill_data_library.rst
.. include:: commands/training_generate_from_wf.rst
.. include:: commands/training_init.rst
.. include:: commands/upload_data.rst
.. include:: commands/workflow_convert.rst
.. include:: commands/workflow_edit.rst
.. include:: commands/workflow_job_init.rst
.. include:: commands/workflow_lint.rst
.. include:: commands/workflow_test_init.rst
.. include:: commands/workflow_test_on_invocation.rst
.. include:: commands/workflow_track.rst
.. include:: commands/workflow_upload.rst