Merge ff390ff into 2992334

docs/commands.rst

@@ -23,7 +23,6 @@ documentation describes these commands.
 .. include:: commands/conda_search.rst
 .. include:: commands/config_init.rst
 .. include:: commands/container_register.rst
-.. include:: commands/cwl_script.rst
 .. include:: commands/database_create.rst
 .. include:: commands/database_delete.rst
 .. include:: commands/database_list.rst
@@ -41,7 +40,6 @@ documentation describes these commands.
 .. include:: commands/profile_list.rst
 .. include:: commands/project_init.rst
 .. include:: commands/pull_request.rst
-.. include:: commands/run.rst
 .. include:: commands/serve.rst
 .. include:: commands/share_test.rst
 .. include:: commands/shed_build.rst
@@ -58,6 +56,9 @@ documentation describes these commands.
 .. include:: commands/test_reports.rst
 .. include:: commands/tool_factory.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/travis_init.rst
 .. include:: commands/virtualenv.rst
 .. include:: commands/workflow_convert.rst

docs/commands/training_fill_data_library.rst

@@ -0,0 +1,27 @@
+
+``training_fill_data_library`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``training_fill_data_library``. This help message can be generated with ``planemo training_fill_data_library
+--help``.
+
+**Usage**::
+
+    planemo training_fill_data_library [OPTIONS] TOOL_PATH
+
+**Help**
+
+Build training template from workflow.
+**Options**::
+
+
+      --topic_name TEXT     Name (directory name) of the topic to create or in which
+                            a tutorial should be created or updates  [required]
+      --tutorial_name TEXT  Name (directory name) of the tutorial to modify
+                            [required]
+      --zenodo_link TEXT    Zenodo URL with the input data
+      --datatypes PATH      YAML file with the correspondance between Zenodo
+                            extension and Galaxy datatypes
+      --help                Show this message and exit.
+    

docs/commands/training_generate_from_wf.rst

@@ -0,0 +1,171 @@
+
+``training_generate_from_wf`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``training_generate_from_wf``. This help message can be generated with ``planemo training_generate_from_wf
+--help``.
+
+**Usage**::
+
+    planemo training_generate_from_wf [OPTIONS] TOOL_PATH
+
+**Help**
+
+Create tutorial skeleton from workflow.
+**Options**::
+
+
+      --topic_name TEXT               Name (directory name) of the topic to create
+                                      or in which a tutorial should be created or
+                                      updates  [required]
+      --tutorial_name TEXT            Name (directory name) of the tutorial to
+                                      modify  [required]
+      --workflow PATH                 Workflow of the tutorial (locally)
+      --galaxy_url TEXT               URL of a Galaxy instance with the workflow
+      --galaxy_api_key TEXT           API key on the Galaxy instance with the
+                                      workflow
+      --workflow_id TEXT              ID of the workflow on the Galaxy instance
+      --galaxy_root DIRECTORY         Root of development galaxy directory to
+                                      execute command with.
+      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
+      --extra_tools PATH              Extra tool sources to include in Galaxy's tool
+                                      panel (file or directory). These will not be
+                                      linted/tested/etc... but they will be
+                                      available to workflows and for interactive
+                                      use.
+      --install_galaxy                Download and configure a disposable copy of
+                                      Galaxy from github.
+      --galaxy_branch TEXT            Branch of Galaxy to target (defaults to
+                                      master) if a Galaxy root isn't specified.
+      --galaxy_source TEXT            Git source of Galaxy to target (defaults to
+                                      the official galaxyproject github source if a
+                                      Galaxy root isn't specified.
+      --skip_venv                     Do not create or source a virtualenv
+                                      environment for Galaxy, this should be used or
+                                      instance to preserve an externally configured
+                                      virtual environment or conda environment.
+      --no_cache_galaxy               Skip caching of Galaxy source and dependencies
+                                      obtained with --install_galaxy. Not caching
+                                      this results in faster downloads (no git) - so
+                                      is better on throw away instances such with
+                                      TravisCI.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
+      --galaxy_email TEXT             E-mail address to use when launching single-
+                                      user Galaxy server.
+      --docker / --no_docker          Run Galaxy tools in Docker if enabled.
+      --docker_cmd TEXT               Command used to launch docker (defaults to
+                                      docker).
+      --docker_sudo / --no_docker_sudo
+                                      Flag to use sudo when running docker.
+      --docker_host TEXT              Docker host to target when executing docker
+                                      commands (defaults to localhost).
+      --docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
+                                      enabled (defaults to sudo).
+      --mulled_containers, --biocontainers
+                                      Test tools against mulled containers (forces
+                                      --docker).
+      --job_config_file PATH          Job configuration file for Galaxy to target.
+      --tool_dependency_dir DIRECTORY
+                                      Tool dependency dir for Galaxy to target.
+      --port INTEGER                  Port to serve Galaxy on (default is 9090).
+      --host TEXT                     Host to bind Galaxy to. Default is 127.0.0.1
+                                      that is restricted to localhost connections
+                                      for security reasons set to 0.0.0.0 to bind
+                                      Galaxy to all ports including potentially
+                                      publicly accessible ones.
+      --engine [galaxy|docker_galaxy|external_galaxy]
+                                      Select an engine to serve aritfacts such as
+                                      tools and workflows. Defaults to a local
+                                      Galaxy, but running Galaxy within a Docker
+                                      container.
+      --non_strict_cwl                Disable strict validation of CWL.
+      --docker_galaxy_image TEXT      Docker image identifier for docker-galaxy-
+                                      flavor used if engine type is specified as
+                                      ``docker-galaxy``. Defaults to
+                                      quay.io/bgruening/galaxy.
+      --docker_extra_volume PATH      Extra path to mount if --engine docker.
+      --test_data DIRECTORY           test-data directory to for specified tool(s).
+      --tool_data_table PATH          tool_data_table_conf.xml file to for specified
+                                      tool(s).
+      --dependency_resolvers_config_file PATH
+                                      Dependency resolver configuration for Galaxy
+                                      to target.
+      --brew_dependency_resolution    Configure Galaxy to use plain brew dependency
+                                      resolution.
+      --shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
+                                      dependency resolution.
+      --no_dependency_resolution      Configure Galaxy with no dependency resolvers.
+      --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
+                                      commands.
+      --conda_exec PATH               Location of conda executable.
+      --conda_debug                   Enable more verbose conda logging.
+      --conda_channels, --conda_ensure_channels TEXT
+                                      Ensure conda is configured with specified
+                                      comma separated list of channels.
+      --conda_use_local               Use locally built packages while building
+                                      Conda environments.
+      --conda_dependency_resolution   Configure Galaxy to use only conda for
+                                      dependency resolution.
+      --conda_copy_dependencies       Conda dependency resolution for Galaxy will
+                                      copy dependencies instead of attempting to
+                                      link them.
+      --conda_auto_install / --no_conda_auto_install
+                                      Conda dependency resolution for Galaxy will
+                                      attempt to install requested but missing
+                                      packages.
+      --conda_auto_init / --no_conda_auto_init
+                                      Conda dependency resolution for Galaxy will
+                                      auto install conda itself using miniconda if
+                                      not availabe on conda_prefix.
+      --profile TEXT                  Name of profile (created with the
+                                      profile_create command) to use with this
+                                      command.
+      --postgres                      Use postgres database type.
+      --database_type [postgres|postgres_docker|sqlite|auto]
+                                      Type of database to use for profile - 'auto',
+                                      'sqlite', 'postgres', and 'postgres_docker'
+                                      are available options. Use postgres to use an
+                                      existing postgres server you user can access
+                                      without a password via the psql command. Use
+                                      postgres_docker to have Planemo manage a
+                                      docker container running postgres. Data with
+                                      postgres_docker is not yet persisted past when
+                                      you restart the docker container launched by
+                                      Planemo so be careful with this option.
+      --postgres_psql_path TEXT       Name or or path to postgres client binary
+                                      (psql).
+      --postgres_database_user TEXT   Postgres username for managed development
+                                      databases.
+      --postgres_database_host TEXT   Postgres host name for managed development
+                                      databases.
+      --postgres_database_port TEXT   Postgres port for managed development
+                                      databases.
+      --file_path DIRECTORY           Location for files created by Galaxy (e.g.
+                                      database/files).
+      --database_connection TEXT      Database connection string to use for Galaxy.
+      --shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
+      --shed_tool_path TEXT           Location of shed tools directory for Galaxy.
+      --galaxy_single_user / --no_galaxy_single_user
+                                      By default Planemo will configure Galaxy to
+                                      run in single-user mode where there is just
+                                      one user and this user is automatically logged
+                                      it. Use --no_galaxy_single_user to prevent
+                                      Galaxy from running this way.
+      --daemon                        Serve Galaxy process as a daemon.
+      --pid_file PATH                 Location of pid file is executed with
+                                      --daemon.
+      --ignore_dependency_problems    When installing shed repositories for
+                                      workflows, ignore dependency issues. These
+                                      likely indicate a problem but in some cases
+                                      may not prevent a workflow from successfully
+                                      executing.
+      --shed_install / --no_shed_install
+                                      By default Planemo will attempt to install
+                                      repositories needed for workflow testing. This
+                                      may not be appropriate for production servers
+                                      and so this can disabled by calling planemo
+                                      with --no_shed_install.
+      --help                          Show this message and exit.
+