Update command docs.

docs/commands.rst

@@ -10,12 +10,16 @@ documentation describes these commands.
 .. include:: commands/brew.rst
 .. include:: commands/brew_env.rst
 .. include:: commands/brew_init.rst
+.. include:: commands/conda_env.rst
+.. include:: commands/conda_init.rst
+.. include:: commands/conda_install.rst
 .. include:: commands/config_init.rst
 .. include:: commands/cwl_run.rst
 .. include:: commands/cwl_script.rst
 .. include:: commands/dependency_script.rst
 .. include:: commands/docker_build.rst
 .. include:: commands/docker_shell.rst
+.. include:: commands/docs.rst
 .. include:: commands/lint.rst
 .. include:: commands/normalize.rst
 .. include:: commands/project_init.rst

docs/commands/conda_env.rst

@@ -0,0 +1,31 @@
+
+``conda_env`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``conda_env``. This help message can be generated with ``planemo conda_env
+--help``.
+
+**Usage**::
+
+    planemo conda_env [OPTIONS] TOOL_PATH
+
+**Help**
+
+Source output to activate a conda environment for this tool.
+
+    % . <(planemo conda_env bowtie2.xml)
+    % which bowtie2
+    TODO_PLACE_PATH_HERE
+
+**Options**::
+
+
+      --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_ensure_channels TEXT  Ensure conda is configured with specified comma
+                                    separated list of channels.
+      --help                        Show this message and exit.
+    

docs/commands/conda_init.rst

@@ -0,0 +1,34 @@
+
+``conda_init`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``conda_init``. This help message can be generated with ``planemo conda_init
+--help``.
+
+**Usage**::
+
+    planemo conda_init [OPTIONS]
+
+**Help**
+
+Download and install conda.
+
+This will download conda for managing dependencies for your platform
+using the appropriate Miniconda installer.
+
+By running this command, you are agreeing to the terms of the conda
+license a 3-clause BSD 3 license. Please review full license at
+http://docs.continuum.io/anaconda/eula.
+
+**Options**::
+
+
+      --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_ensure_channels TEXT  Ensure conda is configured with specified comma
+                                    separated list of channels.
+      --help                        Show this message and exit.
+    

docs/commands/conda_install.rst

@@ -0,0 +1,26 @@
+
+``conda_install`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``conda_install``. This help message can be generated with ``planemo conda_install
+--help``.
+
+**Usage**::
+
+    planemo conda_install [OPTIONS] TOOL_PATH
+
+**Help**
+
+Install conda packages for tool requirements.
+**Options**::
+
+
+      --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_ensure_channels TEXT  Ensure conda is configured with specified comma
+                                    separated list of channels.
+      --help                        Show this message and exit.
+    

docs/commands/cwl_run.rst

@@ -23,18 +23,30 @@ Planemo command for running CWL tools and jobs.
 
       --galaxy_root DIRECTORY         Root of development galaxy directory to
                                       execute command with.
-      --galaxy_sqlite_database DIRECTORY
-                                      Preseeded Galaxy sqlite database to target.
+      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --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.
       --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
@@ -47,12 +59,42 @@ Planemo command for running CWL tools and jobs.
       --dependency_resolvers_config_file PATH
                                       Dependency resolver configuration for Galaxy
                                       to target.
-      --tool_dependency_dir DIRECTORY
-                                      Tool dependency dir 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.
+      --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_ensure_channels TEXT    Ensure conda is configured with specified
+                                      comma separated list of channels.
+      --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            Conda dependency resolution for Galaxy will
+                                      auto install will attempt to install requested
+                                      but missing packages.
+      --conda_auto_init               Conda dependency resolution for Galaxy will
+                                      auto install conda itself using miniconda if
+                                      not availabe on conda_prefix.
+      --profile TEXT                  Location of pid file is executed with
+                                      --daemon.
+      --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.
+      --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.
+      --daemon                        Serve Galaxy process as a daemon.
+      --pid_file TEXT                 Location of pid file is executed with
+                                      --daemon.
       --cwl_galaxy_root DIRECTORY     Root of development galaxy directory to
                                       execute command with (must be branch of Galaxy
                                       with CWL support, this option is experimental

docs/commands/docker_build.rst

@@ -12,7 +12,7 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
-Builds (and optionally caches Docker images) for tool Dockerfiles.
+Build (and optionally cache Docker images) for tool Dockerfiles.
 
 Loads the tool or tools referenced by ``TOOL_PATH`` (by default all tools
 in current directory), and ensures they all reference the same Docker image

docs/commands/docs.rst

@@ -0,0 +1,20 @@
+
+``docs`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``docs``. This help message can be generated with ``planemo docs
+--help``.
+
+**Usage**::
+
+    planemo docs [OPTIONS]
+
+**Help**
+
+Open the Planemo documentation in a web browser.
+**Options**::
+
+
+      --help  Show this message and exit.
+    

docs/commands/lint.rst

@@ -12,9 +12,7 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
-Check specified tool(s) for common errors and adherence to best
-practices.
-
+Check tools for common errors and adherence to best practices.
 **Options**::
 
 

docs/commands/serve.rst

@@ -39,18 +39,30 @@ instances.
 
       --galaxy_root DIRECTORY         Root of development galaxy directory to
                                       execute command with.
-      --galaxy_sqlite_database DIRECTORY
-                                      Preseeded Galaxy sqlite database to target.
+      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --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.
       --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
@@ -63,12 +75,42 @@ instances.
       --dependency_resolvers_config_file PATH
                                       Dependency resolver configuration for Galaxy
                                       to target.
-      --tool_dependency_dir DIRECTORY
-                                      Tool dependency dir 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.
+      --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_ensure_channels TEXT    Ensure conda is configured with specified
+                                      comma separated list of channels.
+      --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            Conda dependency resolution for Galaxy will
+                                      auto install will attempt to install requested
+                                      but missing packages.
+      --conda_auto_init               Conda dependency resolution for Galaxy will
+                                      auto install conda itself using miniconda if
+                                      not availabe on conda_prefix.
+      --profile TEXT                  Location of pid file is executed with
+                                      --daemon.
+      --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.
+      --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.
+      --daemon                        Serve Galaxy process as a daemon.
+      --pid_file TEXT                 Location of pid file is executed with
+                                      --daemon.
       --cwl                           Configure Galaxy for use with CWL tool. (this
                                       option is experimental and will be replaced
                                       when and if CWL support is merged into

docs/commands/shed_lint.rst

@@ -14,7 +14,6 @@ This section is auto-generated from the help text for the planemo command
 
 Check a Tool Shed repository for common problems.
 
-
 With the ``--tools`` flag, this command lints actual Galaxy tools
 in addition to tool shed artifacts.