--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venv/lib/python2.7/site-packages/planemo/options.py	Mon Oct 12 17:43:33 2015 -0400
@@ -0,0 +1,634 @@
+""" Click definitions for various shared options and arguments.
+"""
+
+import functools
+import os
+
+import click
+from galaxy.tools.deps import docker_util
+from .config import get_default_callback
+
+
+def force_option(what="files"):
+    return click.option(
+        "-f",
+        "--force",
+        is_flag=True,
+        help="Overwrite existing %s if present." % what,
+    )
+
+
+def test_data_option():
+    return click.option(
+        "--test_data",
+        type=click.Path(exists=True, file_okay=False, resolve_path=True),
+        help="test-data directory to for specified tool(s).",
+    )
+
+
+def tool_data_table_option():
+    return click.option(
+        "--tool_data_table",
+        type=click.Path(exists=True, file_okay=True, resolve_path=True),
+        help="tool_data_table_conf.xml file to for specified tool(s).",
+    )
+
+
+def galaxy_root_option():
+    return click.option(
+        "--galaxy_root",
+        type=click.Path(exists=True, file_okay=False, resolve_path=True),
+        help="Root of development galaxy directory to execute command with.",
+    )
+
+
+def galaxy_port_option():
+    return click.option(
+        "--port",
+        type=int,
+        default=None,
+        callback=get_default_callback("9090"),
+        help="Port to serve Galaxy on (default is 9090).",
+    )
+
+
+def galaxy_host_option():
+    return click.option(
+        "--host",
+        type=str,
+        default=None,
+        callback=get_default_callback("127.0.0.1"),
+        help=("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."),
+    )
+
+
+def dependency_resolvers_option():
+    return click.option(
+        "--dependency_resolvers_config_file",
+        type=click.Path(
+            exists=True,
+            file_okay=True,
+            dir_okay=False,
+            resolve_path=True
+        ),
+        help="Dependency resolver configuration for Galaxy to target.",
+    )
+
+
+def brew_dependency_resolution():
+    return click.option(
+        "--brew_dependency_resolution",
+        is_flag=True,
+        help="Configure Galaxy to use plain brew dependency resolution.",
+    )
+
+
+def shed_dependency_resolution():
+    return click.option(
+        "--shed_dependency_resolution",
+        is_flag=True,
+        help=("Configure Galaxy to use brewed Tool Shed dependency"
+              " resolution."),
+    )
+
+
+def job_config_option():
+    return click.option(
+        "--job_config_file",
+        type=click.Path(
+            exists=True,
+            file_okay=True,
+            dir_okay=False,
+            resolve_path=True
+        ),
+        help="Job configuration file for Galaxy to target.",
+    )
+
+
+def tool_dependency_dir_option():
+    return click.option(
+        "--tool_dependency_dir",
+        type=click.Path(
+            exists=True,
+            file_okay=False,
+            dir_okay=True,
+            resolve_path=True
+        ),
+        help="Tool dependency dir for Galaxy to target.",
+    )
+
+
+def install_galaxy_option():
+    return click.option(
+        "--install_galaxy",
+        is_flag=True,
+        help="Download and configure a disposable copy of Galaxy from github."
+    )
+
+
+def no_cache_galaxy_option():
+    return click.option(
+        "--no_cache_galaxy",
+        is_flag=True,
+        help=("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. ")
+    )
+
+
+def brew_option():
+    return click.option(
+        "--brew",
+        type=click.Path(exists=True, file_okay=True, dir_okay=False),
+        help="Homebrew 'brew' executable to use."
+    )
+
+
+def required_tool_arg():
+    """ Decorate click method as requiring the path to a single tool.
+    """
+    arg_type = click.Path(
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        readable=True,
+        resolve_path=True,
+    )
+    return click.argument("path", metavar="TOOL_PATH", type=arg_type)
+
+
+def _optional_tools_default(ctx, param, value):
+    if param.name == "paths" and len(value) == 0:
+        return [os.path.abspath(os.getcwd())]
+    else:
+        return value
+
+
+def optional_tools_arg(multiple=False):
+    """ Decorate click method as optionally taking in the path to a tool
+    or directory of tools. If no such argument is given the current working
+    directory will be treated as a directory of tools.
+    """
+    arg_type = click.Path(
+        exists=True,
+        file_okay=True,
+        dir_okay=True,
+        readable=True,
+        resolve_path=True,
+    )
+    name = "paths" if multiple else "path"
+    nargs = -1 if multiple else 1
+    return click.argument(
+        name,
+        metavar="TOOL_PATH",
+        type=arg_type,
+        nargs=nargs,
+        callback=_optional_tools_default,
+    )
+
+
+class ProjectOrRepositry(click.Path):
+
+    def __init__(self, **kwds):
+        super(ProjectOrRepositry, self).__init__(**kwds)
+
+    def convert(self, value, param, ctx):
+        if value and value.startswith("git:") or value.startswith("git+"):
+            return value
+        else:
+            return super(ProjectOrRepositry, self).convert(value, param, ctx)
+
+
+def shed_project_arg(multiple=True):
+    arg_type = ProjectOrRepositry(
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        resolve_path=True,
+    )
+    name = "paths" if multiple else "path"
+    nargs = -1 if multiple else 1
+    return click.argument(
+        name,
+        metavar="PROJECT",
+        default=".",
+        type=arg_type,
+        nargs=nargs,
+        callback=_optional_tools_default,
+    )
+
+
+def optional_project_arg(exists=True):
+    arg_type = click.Path(
+        exists=exists,
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        resolve_path=True,
+    )
+    return click.argument(
+        "path",
+        metavar="PROJECT",
+        default=".",
+        type=arg_type
+    )
+
+
+def no_cleanup_option():
+    return click.option(
+        "--no_cleanup",
+        is_flag=True,
+        help=("Do not cleanup temp files created for and by Galaxy.")
+    )
+
+
+def docker_cmd_option():
+    return click.option(
+        "--docker_cmd",
+        default=docker_util.DEFAULT_DOCKER_COMMAND,
+        help="Command used to launch docker (defaults to docker)."
+    )
+
+
+def docker_sudo_option():
+    return click.option(
+        "--docker_sudo",
+        is_flag=True,
+        help="Flag to use sudo when running docker."
+    )
+
+
+def docker_sudo_cmd_option():
+    return click.option(
+        "--docker_sudo_cmd",
+        default=None,
+        help="sudo command to use when --docker_sudo is enabled " +
+             "(defaults to sudo).",
+        callback=get_default_callback(docker_util.DEFAULT_SUDO_COMMAND),
+    )
+
+
+def docker_host_option():
+    return click.option(
+        "--docker_host",
+        default=None,
+        help="Docker host to target when executing docker commands " +
+             "(defaults to localhost).",
+        callback=get_default_callback(docker_util.DEFAULT_HOST),
+    )
+
+
+def shed_owner_option():
+    return click.option(
+        "--owner",
+        help="Tool Shed repository owner (username)."
+    )
+
+
+def shed_name_option():
+    return click.option(
+        "--name",
+        help="Tool Shed repository name (defaults to the inferred "
+             "tool directory name)."
+    )
+
+
+def validate_shed_target_callback(ctx, param, value):
+    target = get_default_callback("toolshed")(ctx, param, value)
+    if target is None:
+        ctx.fail("default_shed_target set to None, must specify a value for "
+                 "--shed_target to run this command.")
+    return target
+
+
+def shed_target_option():
+    return click.option(
+        "-t",
+        "--shed_target",
+        help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
+             "'local' (alias for http://localhost:9009/), an arbitrary url "
+             "or mappings defined ~/.planemo.yml.",
+        default=None,
+        callback=validate_shed_target_callback,
+    )
+
+
+def shed_key_option():
+    return click.option(
+        "--shed_key",
+        help=("API key for Tool Shed access. An API key is required unless "
+              "e-mail and password is specified. This key can be specified "
+              "with either --shed_key or --shed_key_from_env.")
+    )
+
+
+def shed_key_from_env_option():
+    return click.option(
+        "--shed_key_from_env",
+        help="Environment variable to read API key for Tool Shed access from."
+    )
+
+
+def shed_email_option():
+    return click.option(
+        "--shed_email",
+        help="E-mail for Tool Shed auth (required unless shed_key is "
+             "specified)."
+    )
+
+
+def shed_password_option():
+    return click.option(
+        "--shed_password",
+        help="Password for Tool Shed auth (required unless shed_key is "
+             "specified)."
+    )
+
+
+def shed_skip_upload():
+    return click.option(
+        "--skip_upload",
+        is_flag=True,
+        help=("Skip upload contents as part of operation, only update "
+              "metadata.")
+    )
+
+
+def shed_skip_metadata():
+    return click.option(
+        "--skip_metadata",
+        is_flag=True,
+        help=("Skip metadata update as part of operation, only upload "
+              "new contents.")
+    )
+
+
+def shed_message_option():
+    return click.option(
+        "-m",
+        "--message",
+        help="Commit message for tool shed upload."
+    )
+
+
+def shed_force_create_option():
+    return click.option(
+        "--force_repository_creation",
+        help=("If a repository cannot be found for the specified user/repo "
+              "name pair, then automatically create the repository in the "
+              "toolshed."),
+        is_flag=True,
+        default=False
+    )
+
+
+def shed_check_diff_option():
+    return click.option(
+        "--check_diff",
+        is_flag=True,
+        help=("Skip uploading if the shed_diff detects there would be no "
+              "'difference' (only attributes populated by the shed would "
+              "be updated.)")
+    )
+
+
+def shed_upload_options():
+    return _compose(
+        shed_message_option(),
+        shed_force_create_option(),
+        shed_check_diff_option(),
+    )
+
+
+def shed_realization_options():
+    return _compose(
+        shed_project_arg(multiple=True),
+        recursive_shed_option(),
+        shed_fail_fast_option(),
+    )
+
+
+def shed_repo_options():
+    return _compose(
+        shed_owner_option(),
+        shed_name_option(),
+    )
+
+
+def shed_publish_options():
+    """ Common options for commands that require publishing to a
+    a shed.
+    """
+    return _compose(
+        shed_realization_options(),
+        shed_repo_options(),
+        shed_target_options(),
+    )
+
+
+def shed_read_options():
+    """ Common options that require read access to mapped repositories
+    in a shed.
+    """
+    return _compose(
+        shed_realization_options(),
+        shed_repo_options(),
+        shed_target_options(),
+    )
+
+
+def shed_target_options():
+    """ Common options for commands that require read-only
+    interactions with a shed.
+    """
+    return _compose(
+        shed_email_option(),
+        shed_key_option(),
+        shed_key_from_env_option(),
+        shed_password_option(),
+        shed_target_option(),
+    )
+
+
+def galaxy_run_options():
+    return _compose(
+        galaxy_target_options(),
+        galaxy_port_option(),
+        galaxy_host_option(),
+    )
+
+
+def galaxy_config_options():
+    return _compose(
+        test_data_option(),
+        tool_data_table_option(),
+        dependency_resolvers_option(),
+        tool_dependency_dir_option(),
+        brew_dependency_resolution(),
+        shed_dependency_resolution(),
+    )
+
+
+def galaxy_target_options():
+    return _compose(
+        galaxy_root_option(),
+        install_galaxy_option(),
+        no_cache_galaxy_option(),
+        no_cleanup_option(),
+        job_config_option(),
+    )
+
+
+def galaxy_serve_options():
+    return _compose(
+        galaxy_run_options(),
+        galaxy_config_options(),
+    )
+
+
+def shed_fail_fast_option():
+    return click.option(
+        "--fail_fast",
+        is_flag=True,
+        default=False,
+        help="If multiple repositories are specified and an error occurs "
+             "stop immediately instead of processing remaining repositories."
+    )
+
+
+def lint_xsd_option():
+    return click.option(
+        "--xsd",
+        is_flag=True,
+        default=False,
+        help=("Include experimental tool XSD validation in linting "
+              "process (requires xmllint on PATH or lxml installed).")
+    )
+
+
+def report_level_option():
+    return click.option(
+        "--report_level",
+        type=click.Choice(["all", "warn", "error"]),
+        default="all",
+    )
+
+
+def skip_option():
+    return click.option(
+        "-s",
+        "--skip",
+        default=None,
+        help=("Comma-separated list of lint tests to skip (e.g send ."
+              "--skip 'citations,xml_order' to skip linting of citations "
+              "and best-practice XML ordering.")
+    )
+
+
+def fail_level_option():
+    return click.option(
+        "--fail_level",
+        type=click.Choice(['warn', 'error']),
+        default="warn"
+    )
+
+
+def recursive_shed_option():
+    return recursive_option(
+        "Recursively perform command for nested repository directories.",
+    )
+
+
+def recursive_option(help="Recursively perform command for subdirectories."):
+    return click.option(
+        "-r",
+        "--recursive",
+        is_flag=True,
+        help=help,
+    )
+
+
+def test_options():
+    return _compose(
+        click.option(
+            "--update_test_data",
+            is_flag=True,
+            help="Update test-data directory with job outputs (normally"
+                 " written to directory --job_output_files if specified.)"
+        ),
+        click.option(
+            "--test_output",
+            type=click.Path(file_okay=True, resolve_path=True),
+            callback=get_default_callback("tool_test_output.html"),
+            help=("Output test report (HTML - for humans) defaults to "
+                  "tool_test_output.html."),
+            default=None,
+        ),
+        click.option(
+            "--test_output_text",
+            type=click.Path(file_okay=True, resolve_path=True),
+            callback=get_default_callback(None),
+            help=("Output test report (Basic text - for display in CI)"),
+            default=None,
+        ),
+        click.option(
+            "--test_output_markdown",
+            type=click.Path(file_okay=True, resolve_path=True),
+            callback=get_default_callback(None),
+            help=("Output test report (Markdown style - for humans & "
+                  "computers)"),
+            default=None,
+        ),
+        click.option(
+            "--test_output_xunit",
+            type=click.Path(file_okay=True, resolve_path=True),
+            callback=get_default_callback(None),
+            help="Output test report (xUnit style - for computers).",
+            default=None,
+        ),
+        click.option(
+            "--test_output_json",
+            type=click.Path(file_okay=True, resolve_path=True),
+            callback=get_default_callback("tool_test_output.json"),
+            help=("Output test report (planemo json) defaults to "
+                  "tool_test_output.json."),
+            default=None,
+        ),
+        click.option(
+            "--job_output_files",
+            type=click.Path(file_okay=False, resolve_path=True),
+            help="Write job outputs to specified directory.",
+            default=None,
+        ),
+        click.option(
+            "--summary",
+            type=click.Choice(["none", "minimal", "compact"]),
+            default="minimal",
+            help=("Summary style printed to planemo's standard output (see "
+                  "output reports for more complete summary). Set to 'none' "
+                  "to disable completely.")
+        )
+    )
+
+
+def _compose(*functions):
+    def compose2(f, g):
+        return lambda x: f(g(x))
+    return functools.reduce(compose2, functions)
+
+
+def dependencies_script_options():
+    return _compose(
+        click.option(
+            "--download_cache",
+            type=click.Path(file_okay=False, resolve_path=True),
+            callback=get_default_callback(None),
+            help=("Directory to cache downloaded files, default is $DOWNLOAD_CACHE"),
+            default=None,
+        ),
+    )