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def conda_exec_option():
return planemo_option(
"--conda_exec",
use_global_config=True,
type=click.Path(exists=True, file_okay=True, dir_okay=False),
help="Location of conda executable."
)
def galaxy_email_option():
return planemo_option(
"--galaxy_email",
type=str,
default="planemo@galaxyproject.org",
use_global_config=True,
use_env_var=True,
help="E-mail address to use when launching single-user Galaxy server.",
)
def docker_sudo_cmd_option():
return planemo_option(
"--docker_sudo_cmd",
help="sudo command to use when --docker_sudo is enabled " +
"(defaults to sudo).",
default=docker_util.DEFAULT_SUDO_COMMAND,
use_global_config=True,
)
def install_galaxy_option():
return planemo_option(
"--install_galaxy",
is_flag=True,
help="Download and configure a disposable copy of Galaxy from github."
)
def shed_target_option():
return planemo_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,
use_global_config=True,
callback=validate_shed_target_callback,
)
def shed_message_option():
return planemo_option(
"-m",
"--message",
help="Commit message for tool shed upload."
)
def galaxy_host_option():
return planemo_option(
"--host",
type=str,
default="127.0.0.1",
use_global_config=True,
help=("Host to bind Galaxy to. Default is 127.0.0.1 that is "
"restricted to localhost connections for security reasons "
def database_source_options():
"""Database connection options for commands that utilize a database."""
return _compose(
planemo_option(
"--postgres_psql_path",
default="psql",
use_global_config=True,
help=("Name or or path to postgres client binary (psql)."),
),
planemo_option(
"--postgres_database_user",
default="postgres",
use_global_config=True,
help=("Postgres username for managed development databases."),
),
planemo_option(
"--postgres_database_host",
default=None,
use_global_config=True,
help=("Postgres host name for managed development databases."),
),
planemo_option(
"--postgres_database_port",
default=None,
use_global_config=True,
help=("Postgres port for managed development databases."),
def training_zenodo_option():
return planemo_option(
"--zenodo_link",
help="Zenodo URL with the input data")