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 Creating Galaxy Tools
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
Docs
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Index
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Index
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O
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V
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Y
A
action_type (planemo.shed2tap.base.AutoconfAction 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 attribute)
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)
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 attribute)
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_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 attribute)
(planemo.runnable.RunResponse attribute)
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 attribute)
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 attribute)
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 attribute)
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 attribute)
(planemo.context.PlanemoContextInterface attribute)
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_galaxy_datatype() (in module planemo.training.tutorial)
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 attribute)
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_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 attribute)
(planemo.context.PlanemoContextInterface attribute)
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 attribute)
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 attribute)
has_pull_request_for() (planemo.commands.cmd_container_register.RegistryTarget method)
has_tools (planemo.runnable.Runnable attribute)
(planemo.runnable.RunnableType attribute)
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 attribute)
install_args_list_to_runnables() (in module planemo.runnable_resolve)
install_galaxy_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 attribute)
(planemo.runnable.RunResponse attribute)
is_cwl_artifact (planemo.runnable.RunnableType attribute)
is_galaxy_artifact (planemo.runnable.RunnableType attribute)
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 attribute)
is_rev_dirty() (in module planemo.git)
is_single_artifact (planemo.runnable.Runnable attribute)
(planemo.runnable.RunnableType attribute)
is_tool_load_error() (in module planemo.tools)
J
job_config_option() (in module planemo.options)
job_info (planemo.runnable.ErrorRunResponse attribute)
(planemo.runnable.RunResponse attribute)
K
kill_pid_file() (in module planemo.io)
kill_posix() (in module planemo.io)
L
label (planemo.galaxy.test.structures.TestId attribute)
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 attribute)
(planemo.runnable.RunResponse attribute)
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)
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 attribute)
num_tests (planemo.galaxy.test.structures.GalaxyTestResults attribute)
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.SuccessfulRunResponse attribute)
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 attribute)
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_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_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)
Repo (class in planemo.shed2tap.base)
report_level_option() (in module planemo.options)
report_xunit() (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 attribute)
(planemo.runnable.RunResponse attribute)
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 attribute)
test_data_option() (in module planemo.options)
test_data_search_path (planemo.runnable.Runnable attribute)
test_option() (in module planemo.commands.cmd_autoupdate)
test_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 attribute)
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 attribute)
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_datatype_option() (in module planemo.options)
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 attribute)
(planemo.runnable.RunResponse attribute)
(planemo.runnable.SuccessfulRunResponse attribute)
workflow_output_artifact() (in module planemo.options)
WorkflowLintContext (class in planemo.workflow_lint)
workspace (planemo.context.PlanemoContext attribute)
(planemo.context.PlanemoContextInterface attribute)
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 attribute)
Y
yield_tool_sources() (in module planemo.tools)
yield_tool_sources_on_paths() (in module planemo.tools)
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