Planemo
master
Quick Start
Installation
Configuration
Virtual Appliance
Building Galaxy Tools
Building Common Workflow Language Tools
Publishing to the Tool Shed
Test Format
Best Practices for Maintaining Galaxy Workflows
Running Galaxy workflows
Automating Galaxy Workflows
Autoupdating tools
Commands
FAQs
Galaxy Tool Framework Changes
Code of Conduct
Contributing
Project Governance
Release Checklist
History
Planemo
Index
Edit on GitHub
Index
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F
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V
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W
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Y
A
action_type (planemo.shed2tap.base.AutoconfAction attribute)
(planemo.shed2tap.base.BaseAction attribute)
(planemo.shed2tap.base.ChangeDirectoryAction attribute)
(planemo.shed2tap.base.ChmodAction attribute)
(planemo.shed2tap.base.DownloadBinary attribute)
(planemo.shed2tap.base.DownloadByUrlAction attribute)
(planemo.shed2tap.base.DownloadFileAction attribute)
(planemo.shed2tap.base.MakeDirectoryAction attribute)
(planemo.shed2tap.base.MakeInstallAction attribute)
(planemo.shed2tap.base.MoveDirectoryFilesAction attribute)
(planemo.shed2tap.base.MoveFileAction attribute)
(planemo.shed2tap.base.SetEnvironmentAction attribute)
(planemo.shed2tap.base.SetEnvironmentForInstallAction attribute)
(planemo.shed2tap.base.SetupPerlEnvironmentAction attribute)
(planemo.shed2tap.base.SetupPythonEnvironmentAction attribute)
(planemo.shed2tap.base.SetupREnvironmentAction attribute)
(planemo.shed2tap.base.SetupRubyEnvironmentAction attribute)
(planemo.shed2tap.base.SetupVirtualenvAction attribute)
(planemo.shed2tap.base.ShellCommandAction attribute)
(planemo.shed2tap.base.TemplateShellCommandAction attribute)
ActionPackage (class in planemo.shed2tap.base)
Actions (class in planemo.shed2tap.base)
add() (in module planemo.git)
add_dir_contents_to_repo() (in module planemo.github_util)
alias_option() (in module planemo.options)
all_tests_passed (planemo.galaxy.test.structures.GalaxyTestResults property)
AllureListener (class in planemo.reports.allure)
AllureWriter (class in planemo.reports.allure)
api_exception_to_message() (in module planemo.shed)
(in module planemo.shed.interface)
args_to_str() (in module planemo.io)
asbool() (in module planemo.shed2tap.base)
assert_valid_tool_id_in_tool_shed() (in module planemo.workflow_lint)
AutoconfAction (class in planemo.shed2tap.base)
autoupdate_tool() (in module planemo.autoupdate)
autoupdate_wf() (in module planemo.autoupdate)
B
BaseAction (class in planemo.shed2tap.base)
BaseEngine (class in planemo.engine.interface)
BasePackage (class in planemo.shed2tap.base)
best_practice_search() (in module planemo.conda)
branch() (in module planemo.git)
brew_dependency_resolution() (in module planemo.options)
brew_option() (in module planemo.options)
build() (in module planemo.tool_builder)
(planemo.galaxy.test.structures.GalaxyTestCommand method)
build_conda_context() (in module planemo.conda)
build_cwl_option() (in module planemo.options)
build_engine() (in module planemo.engine.factory)
build_involucro_context() (in module planemo.mulled)
build_lint_args() (in module planemo.lint)
build_mull_target_kwds() (in module planemo.mulled)
build_report() (in module planemo.reports.build_report)
build_tool_lint_args() (in module planemo.tool_lint)
C
cache_download() (planemo.context.PlanemoContext method)
(planemo.context.PlanemoContextInterface method)
calculate_summary_data() (planemo.test.results.StructuredData method)
calculate_summary_data_if_needed() (planemo.test.results.StructuredData method)
can_run() (planemo.engine.interface.BaseEngine method)
can_write_to_path() (in module planemo.io)
cancel() (planemo.galaxy.ephemeris_sleep.SleepCondition method)
captured_io_for_xunit() (in module planemo.io)
case_id() (in module planemo.galaxy.test.structures)
cases() (in module planemo.runnable)
ChangeDirectoryAction (class in planemo.shed2tap.base)
check_conda() (in module planemo.autoupdate)
check_output() (in module planemo.test)
check_topic_init_tuto() (planemo.training.Training method)
check_uploads_ok_option() (in module planemo.options)
checkout() (in module planemo.git)
ChmodAction (class in planemo.shed2tap.base)
ci_chunk_count_option() (in module planemo.options)
ci_chunk_option() (in module planemo.options)
ci_find_options() (in module planemo.options)
ci_group_tools_option() (in module planemo.options)
ci_output_option() (in module planemo.options)
cleanup() (planemo.engine.interface.BaseEngine method)
(planemo.engine.interface.Engine method)
clone() (in module planemo.git)
clone_fork_branch() (in module planemo.github_util)
clone_target_arg() (in module planemo.commands.cmd_clone)
coalesce_return_codes() (in module planemo.io)
collect_conda_target_lists() (in module planemo.conda)
collect_conda_target_lists_and_tool_paths() (in module planemo.conda)
collect_conda_targets() (in module planemo.conda)
collect_mulled_target_lists() (in module planemo.mulled)
command_clone() (in module planemo.git)
command_function() (in module planemo.cli)
commit() (in module planemo.git)
communicate() (in module planemo.io)
conda_auto_init_option() (in module planemo.options)
conda_auto_install_option() (in module planemo.options)
conda_dependency_resolution() (in module planemo.options)
conda_ensure_channels_option() (in module planemo.options)
conda_exec_option() (in module planemo.options)
conda_global_option() (in module planemo.options)
conda_prefix_option() (in module planemo.options)
conda_target_options() (in module planemo.options)
conda_to_mulled_targets() (in module planemo.mulled)
conda_use_local_option() (in module planemo.options)
conditionally_captured_io() (in module planemo.io)
configure_standard_planemo_logging() (in module planemo.context)
convert() (planemo.options.ProjectOrRepositry method)
(planemo.options.UriLike method)
create_command() (in module planemo.virtualenv)
create_database() (planemo.database.interface.DatabaseSource method)
create_database_source() (in module planemo.database)
(in module planemo.database.factory)
create_hands_on_tutorial() (planemo.training.tutorial.Tutorial method)
create_profile() (in module planemo.galaxy.profiles)
create_release() (in module planemo.github_util)
create_requirement_dict() (in module planemo.autoupdate)
create_token_dict() (in module planemo.autoupdate)
create_topic_structure() (planemo.training.topic.Topic method)
create_tutorial() (planemo.training.tutorial.Tutorial method)
cwl_tool (planemo.runnable.RunnableType attribute)
cwl_workflow (planemo.runnable.RunnableType attribute)
cwltool_no_container_option() (in module planemo.options)
CwlToolEngine (class in planemo.engine.cwltool)
D
daemon_option() (in module planemo.options)
data_manager_conf_path (planemo.runnable.Runnable property)
database_connection_option() (in module planemo.options)
database_identifier_argument() (in module planemo.options)
database_source_options() (in module planemo.options)
database_type_option() (in module planemo.options)
DatabaseSource (class in planemo.database.interface)
delete_database() (planemo.database.interface.DatabaseSource method)
delete_profile() (in module planemo.galaxy.profiles)
Dependencies (class in planemo.shed2tap.base)
dependencies_script_options() (in module planemo.options)
Dependency (class in planemo.shed2tap.base)
dependency_resolvers_option() (in module planemo.options)
describe_outputs() (in module planemo.galaxy.workflows)
diff() (in module planemo.git)
(in module planemo.xml.diff)
diff_and_remove() (in module planemo.shed.diff)
diff_repo() (in module planemo.shed)
directory (planemo.runnable.RunnableType attribute)
docker_cmd_option() (in module planemo.options)
docker_config_options() (in module planemo.options)
docker_enable_option() (in module planemo.options)
docker_extra_volume_option() (in module planemo.options)
docker_galaxy_image_option() (in module planemo.options)
docker_host_args() (in module planemo.docker)
docker_host_option() (in module planemo.options)
docker_run_extra_arguments_option() (in module planemo.options)
docker_sudo_cmd_option() (in module planemo.options)
docker_sudo_option() (in module planemo.options)
DockerizedManagedGalaxyEngine (class in planemo.engine.galaxy)
DockerPostgresDatabaseSource (class in planemo.database.postgres_docker)
download_tar() (in module planemo.shed.interface)
download_tarball() (in module planemo.shed)
DownloadBinary (class in planemo.shed2tap.base)
DownloadByUrlAction (class in planemo.shed2tap.base)
DownloadFileAction (class in planemo.shed2tap.base)
downloads() (planemo.shed2tap.base.Actions method)
dry_run() (in module planemo.options)
dry_run_option() (in module planemo.commands.cmd_autoupdate)
E
enable_cwl_option() (in module planemo.options)
enabled() (planemo.xml.validation.XsdValidator method)
end_datetime (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
Engine (class in planemo.engine.interface)
engine_context() (in module planemo.engine)
(in module planemo.engine.factory)
engine_options() (in module planemo.options)
ensure_dependency_resolvers_conf_configured() (in module planemo.deps)
ensure_gh() (in module planemo.github_util)
ensure_profile() (in module planemo.galaxy.profiles)
ensure_runnables_served() (planemo.engine.galaxy.ExternalGalaxyEngine method)
(planemo.engine.galaxy.LocalManagedGalaxyEngine method)
error() (in module planemo.io)
error_message (planemo.runnable.ErrorRunResponse property)
ErrorRunResponse (class in planemo.runnable)
execute() (in module planemo.galaxy.activity)
exists() (planemo.training.topic.Topic method)
(planemo.training.tutorial.Tutorial method)
exit() (planemo.cli.PlanemoCliContext method)
exit_code (planemo.galaxy.test.structures.GalaxyTestResults property)
ExitCodeException
export_metadata_to_ordered_dict() (planemo.training.topic.Topic method)
export_to_ordered_dict() (planemo.training.utils.Requirement method)
export_workflow_file() (planemo.training.tutorial.Tutorial method)
ExternalGalaxyEngine (class in planemo.engine.galaxy)
extra_tools_option() (in module planemo.options)
F
fail_level_option() (in module planemo.options)
failed_ids (planemo.test.results.StructuredData property)
file_path_option() (in module planemo.options)
fill_data_library() (planemo.training.Training method)
filter_changed_in_commit_option() (in module planemo.options)
filter_exclude_from_option() (in module planemo.options)
filter_exclude_option() (in module planemo.options)
filter_paths() (in module planemo.ci)
(in module planemo.io)
find_cases() (in module planemo.galaxy.test.structures)
find_category_ids() (in module planemo.shed.interface)
find_macros() (in module planemo.autoupdate)
find_matching_directories() (in module planemo.io)
find_potential_workflow_files() (in module planemo.workflow_lint)
find_raw_repositories() (in module planemo.shed)
find_repos_from_tool_id() (in module planemo.workflow_lint)
find_repository() (in module planemo.shed.interface)
find_workflow_descriptions() (in module planemo.workflow_lint)
first_download() (planemo.shed2tap.base.Actions method)
fix_workflow_ga() (in module planemo.autoupdate)
fix_workflow_gxformat2() (in module planemo.autoupdate)
for_collections() (in module planemo.test)
for_each_repository() (in module planemo.shed)
for_path() (in module planemo.runnable)
for_paths() (in module planemo.runnable)
for_runnable_identifier() (in module planemo.runnable_resolve)
for_runnable_identifiers() (in module planemo.runnable_resolve)
force_option() (in module planemo.options)
fork() (in module planemo.github_util)
format_wf_steps() (in module planemo.training.tutorial)
from_api() (planemo.shed2tap.base.Repo static method)
from_elem() (planemo.shed2tap.base.BaseAction class method)
from_invocation() (in module planemo.options)
from_xml() (planemo.shed2tap.base.Repo static method)
G
galaxy_admin_key_option() (in module planemo.options)
galaxy_branch_option() (in module planemo.options)
galaxy_config() (in module planemo.galaxy)
(in module planemo.galaxy.config)
galaxy_config_options() (in module planemo.options)
galaxy_cwl_root_option() (in module planemo.options)
galaxy_datamanager (planemo.runnable.RunnableType attribute)
galaxy_docker_options() (in module planemo.options)
galaxy_email_option() (in module planemo.options)
galaxy_host_option() (in module planemo.options)
galaxy_port_option() (in module planemo.options)
galaxy_profiles_directory (planemo.context.PlanemoContext property)
(planemo.context.PlanemoContextInterface property)
galaxy_python_version() (in module planemo.options)
galaxy_root_option() (in module planemo.options)
galaxy_run_options() (in module planemo.options)
galaxy_serve() (in module planemo.galaxy)
galaxy_serve_options() (in module planemo.options)
galaxy_source_option() (in module planemo.options)
galaxy_startup_timeout_option() (in module planemo.options)
galaxy_target_options() (in module planemo.options)
galaxy_tool (planemo.runnable.RunnableType attribute)
galaxy_url_option() (in module planemo.options)
galaxy_user_key_option() (in module planemo.options)
galaxy_workflow (planemo.runnable.RunnableType attribute)
GalaxyTestCommand (class in planemo.galaxy.test.structures)
GalaxyTestResults (class in planemo.galaxy.test.structures)
generate_dockstore_yaml() (in module planemo.workflow_lint)
generate_tuto_from_wf() (planemo.training.Training method)
get_all_actions() (planemo.shed2tap.base.BasePackage method)
get_dict_value() (in module planemo.test.results)
get_empty_input() (in module planemo.training.tool_input)
get_empty_param() (in module planemo.training.tool_input)
get_file() (planemo.shed2tap.base.Repo method)
get_files_from_zenodo() (planemo.training.tutorial.Tutorial method)
get_formatted_conditional_desc() (planemo.training.tool_input.ToolInput method)
get_formatted_desc() (planemo.training.tool_input.ToolInput method)
get_formatted_inputs() (planemo.training.tool_input.ToolInput method)
get_formatted_other_param_desc() (planemo.training.tool_input.ToolInput method)
get_formatted_repeat_desc() (planemo.training.tool_input.ToolInput method)
get_formatted_section_desc() (planemo.training.tool_input.ToolInput method)
get_free_port() (in module planemo.network_util)
get_gh_env() (in module planemo.github_util)
get_github_config() (in module planemo.github_util)
get_hands_on_boxes_from_local_galaxy() (in module planemo.training.tutorial)
get_hands_on_boxes_from_running_galaxy() (in module planemo.training.tutorial)
get_id (planemo.runnable.RunnableOutput property)
get_input_tool_name() (in module planemo.training.tool_input)
get_lower_param_desc() (planemo.training.tool_input.ToolInput method)
get_newest_tool_id() (in module planemo.autoupdate)
get_option_source() (planemo.context.PlanemoContext method)
(planemo.context.PlanemoContextInterface method)
get_or_create_repository() (in module planemo.github_util)
get_output() (planemo.runnable.RunResponse method)
get_outputs() (in module planemo.runnable)
get_requirements() (in module planemo.autoupdate)
(planemo.training.topic.Topic method)
get_shed_context() (in module planemo.shed)
get_tokens() (in module planemo.autoupdate)
get_tools_to_update() (in module planemo.autoupdate)
get_tuto_metata() (planemo.training.tutorial.Tutorial method)
get_validator() (in module planemo.xml.validation)
get_wf_inputs() (in module planemo.training.tutorial)
get_wf_param_values() (in module planemo.training.tutorial)
get_zenodo_record() (in module planemo.training.tutorial)
gi() (in module planemo.galaxy.api)
git_env_for() (in module planemo.git)
github_branch() (in module planemo.options)
github_namespace() (in module planemo.options)
glob() (in module planemo.glob)
global_config (planemo.context.PlanemoContext property)
(planemo.context.PlanemoContextInterface property)
global_config_path() (in module planemo.config)
group_paths() (in module planemo.ci)
H
handle_lint_complete() (in module planemo.lint)
handle_pull_request() (planemo.commands.cmd_container_register.RegistryTarget method)
handle_report_xunit_kwd() (in module planemo.reports.xunit_handler)
handle_reports() (in module planemo.galaxy.test)
(in module planemo.galaxy.test.actions)
handle_reports_and_summary() (in module planemo.galaxy.test)
(in module planemo.galaxy.test.actions)
handle_tool_load_error() (in module planemo.commands.cmd_autoupdate)
(in module planemo.tool_lint)
handled_runnable_types (planemo.engine.cwltool.CwlToolEngine attribute)
(planemo.engine.interface.BaseEngine attribute)
(planemo.engine.toil.ToilEngine attribute)
has_details (planemo.galaxy.test.structures.GalaxyTestResults property)
has_explicit_set_environments() (planemo.shed2tap.base.BasePackage method)
has_multiple_set_environments() (planemo.shed2tap.base.BasePackage method)
has_no_achitecture_install() (planemo.shed2tap.base.BasePackage method)
has_path (planemo.runnable.Runnable property)
has_pull_request_for() (planemo.commands.cmd_container_register.RegistryTarget method)
has_tools (planemo.runnable.Runnable property)
(planemo.runnable.RunnableType property)
has_workflow() (planemo.training.tutorial.Tutorial method)
history_name() (in module planemo.options)
I
id (planemo.galaxy.test.structures.TestId attribute)
ignore_dependency_problems_option() (in module planemo.options)
import_workflow() (in module planemo.galaxy.workflows)
info() (in module planemo.io)
init() (in module planemo.git)
init_data_lib() (planemo.training.tutorial.Tutorial method)
init_from_dict() (planemo.training.utils.Requirement method)
init_from_existing_tutorial() (planemo.training.tutorial.Tutorial method)
init_from_kwds() (planemo.training.topic.Topic method)
(planemo.training.tutorial.Tutorial method)
init_from_metadata() (planemo.training.topic.Topic method)
init_training() (planemo.training.Training method)
input_ids (planemo.runnable.TestCase property)
install_args_list_to_runnables() (in module planemo.runnable_resolve)
install_galaxy_option() (in module planemo.options)
install_prebuilt_client_option() (in module planemo.options)
install_repository_dependencies_option() (in module planemo.options)
install_resolver_dependencies_option() (in module planemo.options)
install_tool_dependencies_option() (in module planemo.options)
invocation_details (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
is_cwl_artifact (planemo.runnable.RunnableType property)
is_galaxy_artifact (planemo.runnable.RunnableType property)
is_galaxy_engine() (in module planemo.engine)
(in module planemo.engine.factory)
is_optional() (planemo.runnable.RunnableOutput method)
is_remote_workflow_uri (planemo.runnable.Runnable property)
is_rev_dirty() (in module planemo.git)
is_single_artifact (planemo.runnable.Runnable property)
(planemo.runnable.RunnableType property)
is_tool_load_error() (in module planemo.tools)
is_valid_output_expectations() (in module planemo.workflow_lint)
J
job_config_option() (in module planemo.options)
job_info (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
K
kill_pid_file() (in module planemo.io)
kill_posix() (in module planemo.io)
L
label (planemo.galaxy.test.structures.TestId property)
latest_installable_revision() (in module planemo.shed.interface)
lint_biocontainer_registered() (in module planemo.linters.biocontainer_registered)
lint_biocontainers_option() (in module planemo.options)
lint_dois() (in module planemo.lint)
lint_repository() (in module planemo.shed_lint)
lint_requirements_in_conda() (in module planemo.linters.conda_requirements)
lint_tool_dois() (in module planemo.linters.doi)
lint_tool_urls() (in module planemo.linters.urls)
lint_tool_xsd() (in module planemo.linters.xsd)
lint_tools_on_path() (in module planemo.tool_lint)
lint_urls() (in module planemo.lint)
lint_workflow_artifacts_on_paths() (in module planemo.workflow_lint)
lint_xsd() (in module planemo.lint)
lint_xsd_option() (in module planemo.options)
list_cmds() (in module planemo.cli)
list_databases() (planemo.database.interface.DatabaseSource method)
list_profiles() (in module planemo.galaxy.profiles)
load_tool_sources_from_path() (in module planemo.tools)
load_yaml() (in module planemo.training.utils)
LocalManagedGalaxyEngine (class in planemo.engine.galaxy)
LocalPostgresDatabaseSource (class in planemo.database.postgres)
log (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
log() (planemo.context.PlanemoContext method)
(planemo.context.PlanemoContextInterface method)
looks_like_a_workflow() (in module planemo.workflow_lint)
ls_remote() (in module planemo.git)
M
main() (in module planemo.galaxy.ephemeris_sleep)
MakeDirectoryAction (class in planemo.shed2tap.base)
MakeInstallAction (class in planemo.shed2tap.base)
merge_test_json() (in module planemo.options)
merge_xunit() (planemo.galaxy.test.StructuredData method)
(planemo.galaxy.test.structures.StructuredData method)
metadata_file_in_path() (in module planemo.ci)
module
planemo
planemo.autoupdate
planemo.ci
planemo.cli
planemo.commands
planemo.commands.cmd_autoupdate
planemo.commands.cmd_ci_find_repos
planemo.commands.cmd_ci_find_tools
planemo.commands.cmd_ci_setup
planemo.commands.cmd_clone
planemo.commands.cmd_conda_build
planemo.commands.cmd_conda_env
planemo.commands.cmd_conda_init
planemo.commands.cmd_conda_install
planemo.commands.cmd_conda_search
planemo.commands.cmd_config_init
planemo.commands.cmd_container_register
planemo.commands.cmd_create_alias
planemo.commands.cmd_create_gist
planemo.commands.cmd_database_create
planemo.commands.cmd_database_delete
planemo.commands.cmd_database_list
planemo.commands.cmd_delete_alias
planemo.commands.cmd_docker_build
planemo.commands.cmd_docker_shell
planemo.commands.cmd_dockstore_init
planemo.commands.cmd_docs
planemo.commands.cmd_lint
planemo.commands.cmd_list_alias
planemo.commands.cmd_list_invocations
planemo.commands.cmd_list_repos
planemo.commands.cmd_merge_test_reports
planemo.commands.cmd_mull
planemo.commands.cmd_mulled_init
planemo.commands.cmd_normalize
planemo.commands.cmd_open
planemo.commands.cmd_profile_create
planemo.commands.cmd_profile_delete
planemo.commands.cmd_profile_list
planemo.commands.cmd_project_init
planemo.commands.cmd_pull_request
planemo.commands.cmd_rerun
planemo.commands.cmd_run
planemo.commands.cmd_serve
planemo.commands.cmd_share_test
planemo.commands.cmd_shed_build
planemo.commands.cmd_shed_create
planemo.commands.cmd_shed_diff
planemo.commands.cmd_shed_download
planemo.commands.cmd_shed_init
planemo.commands.cmd_shed_lint
planemo.commands.cmd_shed_serve
planemo.commands.cmd_shed_test
planemo.commands.cmd_shed_update
planemo.commands.cmd_shed_upload
planemo.commands.cmd_syntax
planemo.commands.cmd_test
planemo.commands.cmd_test_reports
planemo.commands.cmd_tool_init
planemo.commands.cmd_training_fill_data_library
planemo.commands.cmd_training_generate_from_wf
planemo.commands.cmd_training_init
planemo.commands.cmd_upload_data
planemo.commands.cmd_workflow_convert
planemo.commands.cmd_workflow_edit
planemo.commands.cmd_workflow_job_init
planemo.commands.cmd_workflow_lint
planemo.commands.cmd_workflow_test_init
planemo.commands.cmd_workflow_test_on_invocation
planemo.commands.cmd_workflow_upload
planemo.conda
planemo.config
planemo.context
planemo.cwl
planemo.cwl.run
planemo.cwl.toil
planemo.database
planemo.database.factory
planemo.database.interface
planemo.database.postgres
planemo.database.postgres_docker
planemo.deps
planemo.docker
planemo.engine
planemo.engine.cwltool
planemo.engine.factory
planemo.engine.galaxy
planemo.engine.interface
planemo.engine.test
planemo.engine.toil
planemo.exit_codes
planemo.galaxy
planemo.galaxy.activity
planemo.galaxy.api
planemo.galaxy.config
planemo.galaxy.distro_tools
planemo.galaxy.ephemeris_sleep
planemo.galaxy.profiles
planemo.galaxy.run
planemo.galaxy.serve
planemo.galaxy.test
planemo.galaxy.test.actions
planemo.galaxy.test.structures
planemo.galaxy.workflows
planemo.git
planemo.github_util
planemo.glob
planemo.io
planemo.lint
planemo.linters
planemo.linters.biocontainer_registered
planemo.linters.conda_requirements
planemo.linters.doi
planemo.linters.urls
planemo.linters.xsd
planemo.mulled
planemo.network_util
planemo.options
planemo.reports
planemo.reports.allure
planemo.reports.build_report
planemo.reports.xunit_handler
planemo.runnable
planemo.runnable_resolve
planemo.shed
planemo.shed.diff
planemo.shed.interface
planemo.shed2tap
planemo.shed2tap.base
planemo.shed_lint
planemo.templates
planemo.test
planemo.test.data
planemo.test.results
planemo.tool_builder
planemo.tool_lint
planemo.tools
planemo.training
planemo.training.tool_input
planemo.training.topic
planemo.training.tutorial
planemo.training.utils
planemo.virtualenv
planemo.workflow_lint
planemo.xml
planemo.xml.diff
planemo.xml.validation
MoveDirectoryFilesAction (class in planemo.shed2tap.base)
MoveFileAction (class in planemo.shed2tap.base)
mulled_action_option() (in module planemo.options)
mulled_conda_option() (in module planemo.options)
mulled_container_name() (in module planemo.linters.biocontainer_registered)
mulled_containers_option() (in module planemo.options)
mulled_namespace_option() (in module planemo.options)
mulled_options() (in module planemo.options)
N
name (planemo.galaxy.test.structures.TestId attribute)
name_to_command() (in module planemo.cli)
no_cache_galaxy_option() (in module planemo.options)
no_cleanup_option() (in module planemo.options)
no_dependency_resolution() (in module planemo.options)
no_wait_option() (in module planemo.options)
non_strict_cwl_option() (in module planemo.options)
num (planemo.galaxy.test.structures.TestId attribute)
num_problems (planemo.galaxy.test.structures.GalaxyTestResults property)
num_tests (planemo.galaxy.test.structures.GalaxyTestResults property)
O
open_file_or_standard_output() (in module planemo.io)
open_prs() (in module planemo.commands.cmd_container_register)
optional_project_arg() (in module planemo.options)
optional_tools_arg() (in module planemo.options)
optional_tools_or_packages_arg() (in module planemo.options)
outdated_tools() (in module planemo.autoupdate)
outputs_dict (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
P
parse_action() (planemo.shed2tap.base.BasePackage method)
parse_action_package() (planemo.shed2tap.base.BasePackage method)
parse_action_repo() (planemo.shed2tap.base.BaseAction method)
parse_actions() (planemo.shed2tap.base.BasePackage method)
parse_package_elems() (planemo.shed2tap.base.BaseAction method)
parse_xunit_report() (in module planemo.galaxy.test.structures)
paste_test_data_paths_option() (in module planemo.options)
path (planemo.runnable.Runnable property)
path_to_repo_name() (in module planemo.shed)
perform_required_update() (in module planemo.autoupdate)
pid_file_option() (in module planemo.options)
planemo
module
planemo.autoupdate
module
planemo.ci
module
planemo.cli
module
planemo.commands
module
planemo.commands.cmd_autoupdate
module
planemo.commands.cmd_ci_find_repos
module
planemo.commands.cmd_ci_find_tools
module
planemo.commands.cmd_ci_setup
module
planemo.commands.cmd_clone
module
planemo.commands.cmd_conda_build
module
planemo.commands.cmd_conda_env
module
planemo.commands.cmd_conda_init
module
planemo.commands.cmd_conda_install
module
planemo.commands.cmd_conda_search
module
planemo.commands.cmd_config_init
module
planemo.commands.cmd_container_register
module
planemo.commands.cmd_create_alias
module
planemo.commands.cmd_create_gist
module
planemo.commands.cmd_database_create
module
planemo.commands.cmd_database_delete
module
planemo.commands.cmd_database_list
module
planemo.commands.cmd_delete_alias
module
planemo.commands.cmd_docker_build
module
planemo.commands.cmd_docker_shell
module
planemo.commands.cmd_dockstore_init
module
planemo.commands.cmd_docs
module
planemo.commands.cmd_lint
module
planemo.commands.cmd_list_alias
module
planemo.commands.cmd_list_invocations
module
planemo.commands.cmd_list_repos
module
planemo.commands.cmd_merge_test_reports
module
planemo.commands.cmd_mull
module
planemo.commands.cmd_mulled_init
module
planemo.commands.cmd_normalize
module
planemo.commands.cmd_open
module
planemo.commands.cmd_profile_create
module
planemo.commands.cmd_profile_delete
module
planemo.commands.cmd_profile_list
module
planemo.commands.cmd_project_init
module
planemo.commands.cmd_pull_request
module
planemo.commands.cmd_rerun
module
planemo.commands.cmd_run
module
planemo.commands.cmd_serve
module
planemo.commands.cmd_share_test
module
planemo.commands.cmd_shed_build
module
planemo.commands.cmd_shed_create
module
planemo.commands.cmd_shed_diff
module
planemo.commands.cmd_shed_download
module
planemo.commands.cmd_shed_init
module
planemo.commands.cmd_shed_lint
module
planemo.commands.cmd_shed_serve
module
planemo.commands.cmd_shed_test
module
planemo.commands.cmd_shed_update
module
planemo.commands.cmd_shed_upload
module
planemo.commands.cmd_syntax
module
planemo.commands.cmd_test
module
planemo.commands.cmd_test_reports
module
planemo.commands.cmd_tool_init
module
planemo.commands.cmd_training_fill_data_library
module
planemo.commands.cmd_training_generate_from_wf
module
planemo.commands.cmd_training_init
module
planemo.commands.cmd_upload_data
module
planemo.commands.cmd_workflow_convert
module
planemo.commands.cmd_workflow_edit
module
planemo.commands.cmd_workflow_job_init
module
planemo.commands.cmd_workflow_lint
module
planemo.commands.cmd_workflow_test_init
module
planemo.commands.cmd_workflow_test_on_invocation
module
planemo.commands.cmd_workflow_upload
module
planemo.conda
module
planemo.config
module
planemo.context
module
planemo.cwl
module
planemo.cwl.run
module
planemo.cwl.toil
module
planemo.database
module
planemo.database.factory
module
planemo.database.interface
module
planemo.database.postgres
module
planemo.database.postgres_docker
module
planemo.deps
module
planemo.docker
module
planemo.engine
module
planemo.engine.cwltool
module
planemo.engine.factory
module
planemo.engine.galaxy
module
planemo.engine.interface
module
planemo.engine.test
module
planemo.engine.toil
module
planemo.exit_codes
module
planemo.galaxy
module
planemo.galaxy.activity
module
planemo.galaxy.api
module
planemo.galaxy.config
module
planemo.galaxy.distro_tools
module
planemo.galaxy.ephemeris_sleep
module
planemo.galaxy.profiles
module
planemo.galaxy.run
module
planemo.galaxy.serve
module
planemo.galaxy.test
module
planemo.galaxy.test.actions
module
planemo.galaxy.test.structures
module
planemo.galaxy.workflows
module
planemo.git
module
planemo.github_util
module
planemo.glob
module
planemo.io
module
planemo.lint
module
planemo.linters
module
planemo.linters.biocontainer_registered
module
planemo.linters.conda_requirements
module
planemo.linters.doi
module
planemo.linters.urls
module
planemo.linters.xsd
module
planemo.mulled
module
planemo.network_util
module
planemo.options
module
planemo.reports
module
planemo.reports.allure
module
planemo.reports.build_report
module
planemo.reports.xunit_handler
module
planemo.runnable
module
planemo.runnable_resolve
module
planemo.shed
module
planemo.shed.diff
module
planemo.shed.interface
module
planemo.shed2tap
module
planemo.shed2tap.base
module
planemo.shed_lint
module
planemo.templates
module
planemo.test
module
planemo.test.data
module
planemo.test.results
module
planemo.tool_builder
module
planemo.tool_lint
module
planemo.tools
module
planemo.training
module
planemo.training.tool_input
module
planemo.training.topic
module
planemo.training.tutorial
module
planemo.training.utils
module
planemo.virtualenv
module
planemo.workflow_lint
module
planemo.xml
module
planemo.xml.diff
module
planemo.xml.validation
module
planemo_directory (planemo.context.PlanemoContext attribute)
planemo_option() (in module planemo.config)
PlanemoCliContext (class in planemo.cli)
PlanemoContext (class in planemo.context)
PlanemoContextInterface (class in planemo.context)
postgres_datatype_type_option() (in module planemo.options)
prepare_data_library_from_zenodo() (planemo.training.tutorial.Tutorial method)
print_as_yaml() (in module planemo.ci)
print_path_list() (in module planemo.ci)
process() (planemo.reports.allure.AllureWriter method)
process_test_case() (planemo.reports.allure.AllureWriter method)
profile_database_options() (in module planemo.options)
profile_name_argument() (in module planemo.options)
profile_option() (in module planemo.options)
ProjectOrRepositry (class in planemo.options)
ps1_for_path() (in module planemo.io)
publish_as_gist_file() (in module planemo.github_util)
publish_dockstore_option() (in module planemo.options)
push() (in module planemo.git)
R
read_global_config() (in module planemo.config)
read_summary() (planemo.test.results.StructuredData method)
real_io() (in module planemo.io)
recipe_arg() (in module planemo.options)
recipe_base_name() (planemo.shed2tap.base.Repo method)
recursive_option() (in module planemo.options)
recursive_shed_option() (in module planemo.options)
RegistryTarget (class in planemo.commands.cmd_container_register)
render() (in module planemo.templates)
render_message_to_string() (in module planemo.reports.build_report)
Repo (class in planemo.shed2tap.base)
report_level_option() (in module planemo.options)
report_xunit() (in module planemo.options)
required_invocation_id_arg() (in module planemo.options)
required_job_arg() (in module planemo.options)
required_new_job_arg() (in module planemo.options)
required_runnable_arg() (in module planemo.options)
required_tool_arg() (in module planemo.options)
required_workflow_arg() (in module planemo.options)
Requirement (class in planemo.training.utils)
rerun() (planemo.engine.galaxy.ExternalGalaxyEngine method)
rev() (in module planemo.git)
rev_if_git() (in module planemo.git)
run() (planemo.engine.interface.BaseEngine method)
(planemo.engine.interface.Engine method)
run_cwltool() (in module planemo.cwl)
(in module planemo.cwl.run)
run_download_outputs_option() (in module planemo.options)
run_engine_option() (in module planemo.options)
run_galaxy_command() (in module planemo.galaxy)
(in module planemo.galaxy.run)
run_history_tags_option() (in module planemo.options)
run_output_directory_option() (in module planemo.options)
run_output_json_option() (in module planemo.options)
run_toil() (in module planemo.cwl)
(in module planemo.cwl.toil)
Runnable (class in planemo.runnable)
RunnableOutput (class in planemo.runnable)
RunnableType (class in planemo.runnable)
RunResponse (class in planemo.runnable)
S
same_as() (planemo.shed2tap.base.BaseAction method)
save_to_yaml() (in module planemo.training.utils)
search_tool_path_for() (in module planemo.test.data)
serve() (in module planemo.galaxy.serve)
serve_daemon() (in module planemo.galaxy.serve)
serve_engine_option() (in module planemo.options)
set_default_requirement() (planemo.training.topic.Topic method)
set_dir_name() (planemo.training.tutorial.Tutorial method)
set_exit_code() (planemo.test.results.StructuredData method)
set_option_source() (planemo.context.PlanemoContext method)
(planemo.context.PlanemoContextInterface method)
set_paths() (planemo.training.topic.Topic method)
SetEnvironmentAction (class in planemo.shed2tap.base)
SetEnvironmentForInstallAction (class in planemo.shed2tap.base)
setup_venv() (in module planemo.galaxy)
(in module planemo.galaxy.run)
SetupPerlEnvironmentAction (class in planemo.shed2tap.base)
SetupPythonEnvironmentAction (class in planemo.shed2tap.base)
SetupREnvironmentAction (class in planemo.shed2tap.base)
SetupRubyEnvironmentAction (class in planemo.shed2tap.base)
SetupVirtualenvAction (class in planemo.shed2tap.base)
SetVariable (class in planemo.shed2tap.base)
shed_check_diff_option() (in module planemo.options)
shed_dependency_resolution() (in module planemo.options)
shed_email_option() (in module planemo.options)
shed_fail_fast_option() (in module planemo.options)
shed_force_create_option() (in module planemo.options)
shed_init() (in module planemo.shed)
shed_install() (planemo.engine.galaxy.LocalManagedGalaxyEngine method)
shed_install_option() (in module planemo.options)
shed_key_from_env_option() (in module planemo.options)
shed_key_option() (in module planemo.options)
shed_message_option() (in module planemo.options)
shed_name_option() (in module planemo.options)
shed_owner_option() (in module planemo.options)
shed_password_option() (in module planemo.options)
shed_project_arg() (in module planemo.options)
shed_publish_options() (in module planemo.options)
shed_read_options() (in module planemo.options)
shed_realization_options() (in module planemo.options)
shed_repo_options() (in module planemo.options)
shed_skip_metadata() (in module planemo.options)
shed_skip_upload() (in module planemo.options)
shed_target_option() (in module planemo.options)
shed_target_options() (in module planemo.options)
shed_tools_conf_option() (in module planemo.options)
shed_tools_directory_option() (in module planemo.options)
shed_upload_options() (in module planemo.options)
shell() (in module planemo.io)
shell_join() (in module planemo.io)
ShellCommandAction (class in planemo.shed2tap.base)
simultaneous_upload_option() (in module planemo.options)
single_package() (planemo.shed2tap.base.Dependencies method)
single_user_mode_option() (in module planemo.options)
skip_client_build_option() (in module planemo.options)
skip_install_option() (in module planemo.options)
skip_option() (in module planemo.options)
skip_requirements_option() (in module planemo.commands.cmd_autoupdate)
skip_venv_option() (in module planemo.options)
skiplist_option() (in module planemo.commands.cmd_autoupdate)
sleep() (in module planemo.galaxy.ephemeris_sleep)
SleepCondition (class in planemo.galaxy.ephemeris_sleep)
split_job_and_test() (in module planemo.options)
sqlalchemy_url() (planemo.database.interface.DatabaseSource method)
(planemo.database.postgres.LocalPostgresDatabaseSource method)
(planemo.database.postgres_docker.DockerPostgresDatabaseSource method)
start_datetime (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
stop_gravity() (in module planemo.io)
structured_data() (planemo.runnable.RunResponse method)
structured_test_data() (planemo.runnable.TestCase method)
StructuredData (class in planemo.galaxy.test)
(class in planemo.galaxy.test.structures)
(class in planemo.test.results)
SuccessfulRunResponse (class in planemo.runnable)
T
tee_captured_output() (in module planemo.io)
temp_directory() (in module planemo.io)
template_data() (in module planemo.reports.build_report)
TemplateShellCommandAction (class in planemo.shed2tap.base)
test() (planemo.engine.interface.BaseEngine method)
(planemo.engine.interface.Engine method)
test_data_in_parent_dir (planemo.runnable.RunnableType property)
test_data_option() (in module planemo.options)
test_data_search_path (planemo.runnable.Runnable property)
test_index_option() (in module planemo.options)
test_option() (in module planemo.commands.cmd_autoupdate)
test_options() (in module planemo.options)
test_output_options() (in module planemo.options)
test_report_options() (in module planemo.options)
test_runnables() (in module planemo.engine.test)
TestCase (class in planemo.runnable)
tested_output_ids (planemo.runnable.TestCase property)
TestId (class in planemo.galaxy.test.structures)
text_compare() (in module planemo.xml.diff)
to_bash() (planemo.shed2tap.base.Actions method)
(planemo.shed2tap.base.AutoconfAction method)
(planemo.shed2tap.base.BaseAction method)
(planemo.shed2tap.base.ChangeDirectoryAction method)
(planemo.shed2tap.base.ChmodAction method)
(planemo.shed2tap.base.DownloadByUrlAction method)
(planemo.shed2tap.base.DownloadFileAction method)
(planemo.shed2tap.base.MakeDirectoryAction method)
(planemo.shed2tap.base.MakeInstallAction method)
(planemo.shed2tap.base.MoveDirectoryFilesAction method)
(planemo.shed2tap.base.MoveFileAction method)
(planemo.shed2tap.base.SetEnvironmentAction method)
(planemo.shed2tap.base.SetEnvironmentForInstallAction method)
(planemo.shed2tap.base.ShellCommandAction method)
to_target_str() (in module planemo.commands.cmd_container_register)
ToilEngine (class in planemo.engine.toil)
tool_data_path_option() (in module planemo.options)
tool_data_search_path (planemo.runnable.Runnable property)
tool_data_table_option() (in module planemo.options)
tool_dependency_dir_option() (in module planemo.options)
tool_init_autopygen_option() (in module planemo.options)
tool_init_cite_url_option() (in module planemo.options)
tool_init_command_option() (in module planemo.options)
tool_init_container_option() (in module planemo.options)
tool_init_description_option() (in module planemo.options)
tool_init_doi_option() (in module planemo.options)
tool_init_example_command_option() (in module planemo.options)
tool_init_example_input_option() (in module planemo.options)
tool_init_example_output_option() (in module planemo.options)
tool_init_help_from_command_option() (in module planemo.options)
tool_init_help_text_option() (in module planemo.options)
tool_init_id_option() (in module planemo.options)
tool_init_input_option() (in module planemo.options)
tool_init_macros_option() (in module planemo.options)
tool_init_name_option() (in module planemo.options)
tool_init_named_output_option() (in module planemo.options)
tool_init_output_option() (in module planemo.options)
tool_init_requirement_option() (in module planemo.options)
tool_init_test_case_option() (in module planemo.options)
tool_init_tool_option() (in module planemo.options)
tool_init_version_command_option() (in module planemo.options)
tool_init_version_option() (in module planemo.options)
tool_shed_client() (in module planemo.shed)
tool_shed_instance() (in module planemo.shed.interface)
tool_shed_url() (in module planemo.shed)
tool_source_conda_targets() (in module planemo.conda)
tool_test_json() (in module planemo.options)
ToolDescription (class in planemo.tool_builder)
ToolInput (class in planemo.training.tool_input)
Topic (class in planemo.training.topic)
Training (class in planemo.training)
training_fill_data_library_options() (in module planemo.options)
training_generate_tuto_from_wf_options() (in module planemo.options)
training_init_options() (in module planemo.options)
training_topic (planemo.workflow_lint.WorkflowLintContext attribute)
training_topic_name_option() (in module planemo.options)
training_topic_option() (in module planemo.options)
training_tutorial_name_option() (in module planemo.options)
training_tutorial_name_req_option() (in module planemo.options)
training_tutorial_option() (in module planemo.options)
training_tutorial_worflow_option() (in module planemo.options)
training_zenodo_option() (in module planemo.options)
Tutorial (class in planemo.training.tutorial)
type (planemo.runnable.Runnable attribute)
U
untar_to() (in module planemo.io)
update() (planemo.test.results.StructuredData method)
update_xml() (in module planemo.autoupdate)
uri (planemo.runnable.Runnable attribute)
UriLike (class in planemo.options)
user_api_key() (in module planemo.galaxy.api)
username() (in module planemo.shed.interface)
V
validate() (planemo.xml.validation.XsdValidator method)
validate_shed_target_callback() (in module planemo.options)
vlog() (planemo.context.PlanemoContext method)
(planemo.context.PlanemoContextInterface method)
W
wait_http_service() (in module planemo.network_util)
wait_net_service() (in module planemo.network_util)
wait_on() (in module planemo.io)
warn() (in module planemo.io)
was_successful (planemo.runnable.ErrorRunResponse property)
(planemo.runnable.RunResponse property)
(planemo.runnable.SuccessfulRunResponse property)
workflow_output_artifact() (in module planemo.options)
WorkflowLintContext (class in planemo.workflow_lint)
workspace (planemo.context.PlanemoContext property)
(planemo.context.PlanemoContextInterface property)
write_bibliography() (planemo.training.tutorial.Tutorial method)
write_file() (in module planemo.io)
write_hands_on_tutorial() (planemo.training.tutorial.Tutorial method)
write_results() (in module planemo.reports.allure)
write_targets() (planemo.commands.cmd_container_register.RegistryTarget method)
write_tool_description() (in module planemo.tool_builder)
X
xml_compare() (in module planemo.xml.diff)
XsdValidator (class in planemo.xml.validation)
xunit_t_elements_from_root() (in module planemo.galaxy.test.structures)
xunit_testcase_elements (planemo.galaxy.test.structures.GalaxyTestResults property)
Y
yield_tool_sources() (in module planemo.tools)
yield_tool_sources_on_paths() (in module planemo.tools)
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