Index

_

__init__() (bioblend.galaxy.GalaxyInstance method) (bioblend.toolshed.ToolShedInstance method)

A

add_group_role() (bioblend.galaxy.groups.GroupsClient method) add_group_user() (bioblend.galaxy.groups.GroupsClient method) annotation (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute)

API_MODULE (bioblend.galaxy.objects.wrappers.DatasetCollection attribute) (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute)

B

BASE_ATTRS (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.DatasetCollection attribute) (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.HistoryContentInfo attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetCollectionAssociation attribute) (bioblend.galaxy.objects.wrappers.HistoryPreview attribute) (bioblend.galaxy.objects.wrappers.Job attribute) (bioblend.galaxy.objects.wrappers.Library attribute) (bioblend.galaxy.objects.wrappers.LibraryDatasetDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.Step attribute) (bioblend.galaxy.objects.wrappers.Tool attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) (bioblend.galaxy.objects.wrappers.Wrapper attribute) bioblend module bioblend.config module bioblend.galaxy.config module bioblend.galaxy.dataset_collections module bioblend.galaxy.datasets module bioblend.galaxy.datatypes module bioblend.galaxy.folders module bioblend.galaxy.forms module bioblend.galaxy.ftpfiles module bioblend.galaxy.genomes module bioblend.galaxy.groups module

bioblend.galaxy.histories module bioblend.galaxy.invocations module bioblend.galaxy.jobs module bioblend.galaxy.libraries module bioblend.galaxy.objects.client module bioblend.galaxy.objects.wrappers module bioblend.galaxy.quotas module bioblend.galaxy.roles module bioblend.galaxy.tool_data module bioblend.galaxy.tool_dependencies module bioblend.galaxy.tools module bioblend.galaxy.toolshed module bioblend.galaxy.users module bioblend.galaxy.visual module bioblend.galaxy.workflows module bioblend.toolshed.categories module bioblend.toolshed.repositories module bioblend.toolshed.tools module build() (bioblend.galaxy.tools.ToolClient method)

C

cancel_invocation() (bioblend.galaxy.invocations.InvocationClient method) (bioblend.galaxy.workflows.WorkflowClient method) cancel_job() (bioblend.galaxy.jobs.JobsClient method) clone() (bioblend.galaxy.objects.wrappers.Wrapper method) collection_type (bioblend.galaxy.objects.wrappers.DatasetCollection attribute) CollectionDescription (class in bioblend.galaxy.dataset_collections) CollectionElement (class in bioblend.galaxy.dataset_collections) Config (class in bioblend.config) ConfigClient (class in bioblend.galaxy.config) ConnectionError container (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.DatasetCollection attribute) (bioblend.galaxy.objects.wrappers.Folder attribute) CONTAINER_PREVIEW_TYPE (bioblend.galaxy.objects.client.ObjDatasetContainerClient attribute) (bioblend.galaxy.objects.client.ObjHistoryClient attribute) (bioblend.galaxy.objects.client.ObjLibraryClient attribute) CONTAINER_TYPE (bioblend.galaxy.objects.client.ObjDatasetContainerClient attribute) (bioblend.galaxy.objects.client.ObjHistoryClient attribute) (bioblend.galaxy.objects.client.ObjLibraryClient attribute) CONTENT_INFO_TYPE (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute)

content_infos (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) copy_content() (bioblend.galaxy.histories.HistoryClient method) copy_dataset() (bioblend.galaxy.histories.HistoryClient method) copy_from_dataset() (bioblend.galaxy.libraries.LibraryClient method) (bioblend.galaxy.objects.wrappers.Library method) create() (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) create_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) (bioblend.galaxy.objects.wrappers.History method) create_folder() (bioblend.galaxy.folders.FoldersClient method) (bioblend.galaxy.libraries.LibraryClient method) (bioblend.galaxy.objects.wrappers.Library method) create_form() (bioblend.galaxy.forms.FormsClient method) create_group() (bioblend.galaxy.groups.GroupsClient method) create_history() (bioblend.galaxy.histories.HistoryClient method) create_history_tag() (bioblend.galaxy.histories.HistoryClient method) create_library() (bioblend.galaxy.libraries.LibraryClient method) create_local_user() (bioblend.galaxy.users.UserClient method) create_quota() (bioblend.galaxy.quotas.QuotaClient method) create_remote_user() (bioblend.galaxy.users.UserClient method) create_repository() (bioblend.toolshed.repositories.ToolShedRepositoryClient method) create_role() (bioblend.galaxy.roles.RolesClient method) create_user_apikey() (bioblend.galaxy.users.UserClient method)

D

dag (bioblend.galaxy.objects.wrappers.Workflow attribute) data_collection_input_ids (bioblend.galaxy.objects.wrappers.Workflow property) data_input_ids (bioblend.galaxy.objects.wrappers.Workflow property) Dataset (class in bioblend.galaxy.objects.wrappers) dataset_ids (bioblend.galaxy.objects.wrappers.DatasetContainer property) DatasetClient (class in bioblend.galaxy.datasets) DatasetCollection (class in bioblend.galaxy.objects.wrappers) DatasetCollectionClient (class in bioblend.galaxy.dataset_collections) DatasetContainer (class in bioblend.galaxy.objects.wrappers) DatasetStateException DatasetStateWarning DatatypesClient (class in bioblend.galaxy.datatypes) delete() (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method) (bioblend.galaxy.objects.wrappers.DatasetCollection method) (bioblend.galaxy.objects.wrappers.DatasetContainer method) (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation method) (bioblend.galaxy.objects.wrappers.HistoryDatasetCollectionAssociation method) (bioblend.galaxy.objects.wrappers.Library method) (bioblend.galaxy.objects.wrappers.LibraryDataset method) (bioblend.galaxy.objects.wrappers.Workflow method) delete_data_table() (bioblend.galaxy.tool_data.ToolDataClient method) delete_dataset() (bioblend.galaxy.histories.HistoryClient method) delete_dataset_collection() (bioblend.galaxy.histories.HistoryClient method)

delete_folder() (bioblend.galaxy.folders.FoldersClient method) delete_group_role() (bioblend.galaxy.groups.GroupsClient method) delete_group_user() (bioblend.galaxy.groups.GroupsClient method) delete_history() (bioblend.galaxy.histories.HistoryClient method) delete_library() (bioblend.galaxy.libraries.LibraryClient method) delete_library_dataset() (bioblend.galaxy.libraries.LibraryClient method) delete_quota() (bioblend.galaxy.quotas.QuotaClient method) delete_unused_dependency_paths() (bioblend.galaxy.tool_dependencies.ToolDependenciesClient method) delete_user() (bioblend.galaxy.users.UserClient method) delete_workflow() (bioblend.galaxy.workflows.WorkflowClient method) deleted (bioblend.galaxy.objects.wrappers.DatasetCollection attribute) (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) description (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.Library attribute) download() (bioblend.galaxy.objects.wrappers.Dataset method) (bioblend.galaxy.objects.wrappers.History method) download_dataset() (bioblend.galaxy.datasets.DatasetClient method) download_dataset_collection() (bioblend.galaxy.dataset_collections.DatasetCollectionClient method) download_history() (bioblend.galaxy.histories.HistoryClient method) DS_TYPE (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute) DSC_TYPE (bioblend.galaxy.objects.wrappers.History attribute)

E

elements (bioblend.galaxy.objects.wrappers.HistoryDatasetCollectionAssociation attribute) emit() (bioblend.NullHandler method) export() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.objects.wrappers.Workflow method)

export_history() (bioblend.galaxy.histories.HistoryClient method) export_workflow_dict() (bioblend.galaxy.workflows.WorkflowClient method) export_workflow_to_local_path() (bioblend.galaxy.workflows.WorkflowClient method) extract_workflow_from_history() (bioblend.galaxy.workflows.WorkflowClient method)

F

file_name (bioblend.galaxy.objects.wrappers.LibraryDataset attribute) Folder (class in bioblend.galaxy.objects.wrappers) folder_ids (bioblend.galaxy.objects.wrappers.Library property)

FoldersClient (class in bioblend.galaxy.folders) FormsClient (class in bioblend.galaxy.forms) from_json() (bioblend.galaxy.objects.wrappers.Wrapper class method) FTPFilesClient (class in bioblend.galaxy.ftpfiles)

G

GalaxyInstance (class in bioblend.galaxy) (class in bioblend.galaxy.objects.galaxy_instance) genome_build (bioblend.galaxy.objects.wrappers.Dataset attribute) GenomeClient (class in bioblend.galaxy.genomes) get() (bioblend.galaxy.objects.client.ObjClient method) (bioblend.galaxy.objects.client.ObjDatasetClient method) (bioblend.galaxy.objects.client.ObjDatasetCollectionClient method) (bioblend.galaxy.objects.client.ObjDatasetContainerClient method) (bioblend.galaxy.objects.client.ObjInvocationClient method) (bioblend.galaxy.objects.client.ObjJobClient method) (bioblend.galaxy.objects.client.ObjToolClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method) get_categories() (bioblend.toolshed.categories.ToolShedCategoryClient method) get_citations() (bioblend.galaxy.tools.ToolClient method) get_common_problems() (bioblend.galaxy.jobs.JobsClient method) get_config() (bioblend.galaxy.config.ConfigClient method) get_contents() (bioblend.galaxy.objects.wrappers.Dataset method) get_current_user() (bioblend.galaxy.users.UserClient method) get_data_tables() (bioblend.galaxy.tool_data.ToolDataClient method) get_dataset() (bioblend.galaxy.objects.wrappers.DatasetContainer method) get_dataset_collection() (bioblend.galaxy.objects.wrappers.History method) get_dataset_permissions() (bioblend.galaxy.libraries.LibraryClient method) get_datasets() (bioblend.galaxy.datasets.DatasetClient method) (bioblend.galaxy.objects.wrappers.DatasetContainer method) get_datatypes() (bioblend.galaxy.datatypes.DatatypesClient method) get_destination_params() (bioblend.galaxy.jobs.JobsClient method) get_extra_files() (bioblend.galaxy.histories.HistoryClient method) get_folder() (bioblend.galaxy.objects.wrappers.Library method) get_folders() (bioblend.galaxy.libraries.LibraryClient method) get_forms() (bioblend.galaxy.forms.FormsClient method) get_ftp_files() (bioblend.galaxy.ftpfiles.FTPFilesClient method) get_genomes() (bioblend.galaxy.genomes.GenomeClient method) get_group_roles() (bioblend.galaxy.groups.GroupsClient method) get_group_users() (bioblend.galaxy.groups.GroupsClient method) get_groups() (bioblend.galaxy.groups.GroupsClient method) get_histories() (bioblend.galaxy.histories.HistoryClient method) get_inputs() (bioblend.galaxy.jobs.JobsClient method) get_invocation_biocompute_object() (bioblend.galaxy.invocations.InvocationClient method) get_invocation_report() (bioblend.galaxy.invocations.InvocationClient method) get_invocation_report_pdf() (bioblend.galaxy.invocations.InvocationClient method) get_invocation_step_jobs_summary() (bioblend.galaxy.invocations.InvocationClient method) get_invocation_summary() (bioblend.galaxy.invocations.InvocationClient method) get_invocations() (bioblend.galaxy.invocations.InvocationClient method) (bioblend.galaxy.workflows.WorkflowClient method) get_jobs() (bioblend.galaxy.jobs.JobsClient method) get_libraries() (bioblend.galaxy.libraries.LibraryClient method) get_library_permissions() (bioblend.galaxy.libraries.LibraryClient method)

get_metrics() (bioblend.galaxy.jobs.JobsClient method) get_most_recently_used_history() (bioblend.galaxy.histories.HistoryClient method) get_or_create_user_apikey() (bioblend.galaxy.users.UserClient method) get_ordered_installable_revisions() (bioblend.toolshed.repositories.ToolShedRepositoryClient method) get_outputs() (bioblend.galaxy.jobs.JobsClient method) get_permissions() (bioblend.galaxy.folders.FoldersClient method) get_previews() (bioblend.galaxy.objects.client.ObjClient method) (bioblend.galaxy.objects.client.ObjDatasetClient method) (bioblend.galaxy.objects.client.ObjDatasetCollectionClient method) (bioblend.galaxy.objects.client.ObjDatasetContainerClient method) (bioblend.galaxy.objects.client.ObjInvocationClient method) (bioblend.galaxy.objects.client.ObjJobClient method) (bioblend.galaxy.objects.client.ObjToolClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method) get_published_histories() (bioblend.galaxy.histories.HistoryClient method) get_quotas() (bioblend.galaxy.quotas.QuotaClient method) get_repositories() (bioblend.galaxy.toolshed.ToolShedClient method) (bioblend.toolshed.categories.ToolShedCategoryClient method) (bioblend.toolshed.repositories.ToolShedRepositoryClient method) get_repository_revision_install_info() (bioblend.toolshed.repositories.ToolShedRepositoryClient method) get_roles() (bioblend.galaxy.roles.RolesClient method) get_sniffers() (bioblend.galaxy.datatypes.DatatypesClient method) get_state() (bioblend.galaxy.jobs.JobsClient method) get_status() (bioblend.galaxy.histories.HistoryClient method) get_stream() (bioblend.galaxy.objects.wrappers.Dataset method) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation method) get_tool_panel() (bioblend.galaxy.tools.ToolClient method) get_tools() (bioblend.galaxy.tools.ToolClient method) get_user_apikey() (bioblend.galaxy.users.UserClient method) get_users() (bioblend.galaxy.users.UserClient method) get_version() (bioblend.galaxy.config.ConfigClient method) (in module bioblend) get_visualizations() (bioblend.galaxy.visual.VisualClient method) get_workflow_inputs() (bioblend.galaxy.workflows.WorkflowClient method) get_workflows() (bioblend.galaxy.workflows.WorkflowClient method) gi (bioblend.galaxy.dataset_collections.DatasetCollectionClient attribute) (bioblend.galaxy.datasets.DatasetClient attribute) (bioblend.galaxy.histories.HistoryClient attribute) (bioblend.galaxy.invocations.InvocationClient attribute) (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.DatasetCollection attribute) (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.Tool attribute) (bioblend.galaxy.objects.wrappers.Wrapper attribute) (bioblend.galaxy.tools.ToolClient attribute) (bioblend.toolshed.tools.ToolShedToolClient attribute) GroupsClient (class in bioblend.galaxy.groups)

H

History (class in bioblend.galaxy.objects.wrappers) HistoryClient (class in bioblend.galaxy.histories) HistoryContentInfo (class in bioblend.galaxy.objects.wrappers) HistoryDatasetAssociation (class in bioblend.galaxy.objects.wrappers)

HistoryDatasetCollectionAssociation (class in bioblend.galaxy.objects.wrappers) HistoryDatasetCollectionElement (class in bioblend.galaxy.dataset_collections) HistoryDatasetElement (class in bioblend.galaxy.dataset_collections) HistoryPreview (class in bioblend.galaxy.objects.wrappers)

I

id (bioblend.galaxy.objects.wrappers.Wrapper attribute) import_dataset() (bioblend.galaxy.objects.wrappers.History method) import_history() (bioblend.galaxy.histories.HistoryClient method) import_new() (bioblend.galaxy.objects.client.ObjWorkflowClient method) import_shared() (bioblend.galaxy.objects.client.ObjWorkflowClient method) import_shared_workflow() (bioblend.galaxy.workflows.WorkflowClient method) import_workflow_dict() (bioblend.galaxy.workflows.WorkflowClient method) import_workflow_from_local_path() (bioblend.galaxy.workflows.WorkflowClient method) init_logging() (in module bioblend) input_labels (bioblend.galaxy.objects.wrappers.Workflow property) input_labels_to_ids (bioblend.galaxy.objects.wrappers.Workflow attribute)

input_steps (bioblend.galaxy.objects.wrappers.Step attribute) inputs (bioblend.galaxy.objects.wrappers.Workflow attribute) install_dependencies() (bioblend.galaxy.tools.ToolClient method) install_genome() (bioblend.galaxy.genomes.GenomeClient method) install_repository_revision() (bioblend.galaxy.toolshed.ToolShedClient method) inv_dag (bioblend.galaxy.objects.wrappers.Workflow attribute) InvocationClient (class in bioblend.galaxy.invocations) invoke() (bioblend.galaxy.objects.wrappers.Workflow method) invoke_workflow() (bioblend.galaxy.workflows.WorkflowClient method) is_mapped (bioblend.galaxy.objects.wrappers.Wrapper property) is_modified (bioblend.galaxy.objects.wrappers.Wrapper attribute) is_runnable (bioblend.galaxy.objects.wrappers.Workflow property)

J

Job (class in bioblend.galaxy.objects.wrappers)

JobsClient (class in bioblend.galaxy.jobs)

L

Library (class in bioblend.galaxy.objects.wrappers) LibraryClient (class in bioblend.galaxy.libraries) LibraryContentInfo (class in bioblend.galaxy.objects.wrappers) LibraryDataset (class in bioblend.galaxy.objects.wrappers) LibraryDatasetDatasetAssociation (class in bioblend.galaxy.objects.wrappers) LibraryDatasetElement (class in bioblend.galaxy.dataset_collections) LibraryPreview (class in bioblend.galaxy.objects.wrappers) list() (bioblend.galaxy.objects.client.ObjClient method) (bioblend.galaxy.objects.client.ObjDatasetClient method) (bioblend.galaxy.objects.client.ObjDatasetCollectionClient method) (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjInvocationClient method) (bioblend.galaxy.objects.client.ObjJobClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) (bioblend.galaxy.objects.client.ObjToolClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method)

M

misc_info (bioblend.galaxy.objects.wrappers.Dataset attribute) missing_ids (bioblend.galaxy.objects.wrappers.Workflow attribute) module bioblend bioblend.config bioblend.galaxy.config bioblend.galaxy.dataset_collections bioblend.galaxy.datasets bioblend.galaxy.datatypes bioblend.galaxy.folders bioblend.galaxy.forms bioblend.galaxy.ftpfiles bioblend.galaxy.genomes bioblend.galaxy.groups bioblend.galaxy.histories bioblend.galaxy.invocations bioblend.galaxy.jobs bioblend.galaxy.libraries bioblend.galaxy.objects.client bioblend.galaxy.objects.wrappers bioblend.galaxy.quotas bioblend.galaxy.roles bioblend.galaxy.tool_data bioblend.galaxy.tool_dependencies bioblend.galaxy.tools bioblend.galaxy.toolshed bioblend.galaxy.users bioblend.galaxy.visual bioblend.galaxy.workflows bioblend.toolshed.categories bioblend.toolshed.repositories bioblend.toolshed.tools

module (bioblend.galaxy.config.ConfigClient attribute) (bioblend.galaxy.dataset_collections.DatasetCollectionClient attribute) (bioblend.galaxy.datasets.DatasetClient attribute) (bioblend.galaxy.datatypes.DatatypesClient attribute) (bioblend.galaxy.folders.FoldersClient attribute) (bioblend.galaxy.forms.FormsClient attribute) (bioblend.galaxy.ftpfiles.FTPFilesClient attribute) (bioblend.galaxy.genomes.GenomeClient attribute) (bioblend.galaxy.groups.GroupsClient attribute) (bioblend.galaxy.histories.HistoryClient attribute) (bioblend.galaxy.invocations.InvocationClient attribute) (bioblend.galaxy.jobs.JobsClient attribute) (bioblend.galaxy.libraries.LibraryClient attribute) (bioblend.galaxy.quotas.QuotaClient attribute) (bioblend.galaxy.roles.RolesClient attribute) (bioblend.galaxy.tool_data.ToolDataClient attribute) (bioblend.galaxy.tool_dependencies.ToolDependenciesClient attribute) (bioblend.galaxy.tools.ToolClient attribute) (bioblend.galaxy.toolshed.ToolShedClient attribute) (bioblend.galaxy.users.UserClient attribute) (bioblend.galaxy.visual.VisualClient attribute) (bioblend.galaxy.workflows.WorkflowClient attribute) (bioblend.toolshed.categories.ToolShedCategoryClient attribute) (bioblend.toolshed.repositories.ToolShedRepositoryClient attribute) (bioblend.toolshed.tools.ToolShedToolClient attribute)

N

name (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute)

NotReady NullHandler (class in bioblend)

O

obj_gi_client (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) ObjClient (class in bioblend.galaxy.objects.client) ObjDatasetClient (class in bioblend.galaxy.objects.client) ObjDatasetCollectionClient (class in bioblend.galaxy.objects.client) ObjDatasetContainerClient (class in bioblend.galaxy.objects.client) ObjHistoryClient (class in bioblend.galaxy.objects.client) ObjInvocationClient (class in bioblend.galaxy.objects.client)

ObjJobClient (class in bioblend.galaxy.objects.client) ObjLibraryClient (class in bioblend.galaxy.objects.client) ObjToolClient (class in bioblend.galaxy.objects.client) ObjWorkflowClient (class in bioblend.galaxy.objects.client) open_history() (bioblend.galaxy.histories.HistoryClient method) owner (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute)

P

parameter_input_ids (bioblend.galaxy.objects.wrappers.Workflow property) parent (bioblend.galaxy.objects.wrappers.Folder property) (bioblend.galaxy.objects.wrappers.Wrapper property) paste_content() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.tools.ToolClient method) peek() (bioblend.galaxy.objects.wrappers.Dataset method) POLLING_INTERVAL (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.Tool attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute)

post_to_fetch() (bioblend.galaxy.tools.ToolClient method) preview() (bioblend.galaxy.objects.wrappers.DatasetContainer method) (bioblend.galaxy.objects.wrappers.Workflow method) publish_dataset() (bioblend.galaxy.datasets.DatasetClient method) published (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) purged (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) put_url() (bioblend.galaxy.tools.ToolClient method)

Q

QuotaClient (class in bioblend.galaxy.quotas)

R

refactor_workflow() (bioblend.galaxy.workflows.WorkflowClient method) refresh() (bioblend.galaxy.objects.wrappers.Dataset method) (bioblend.galaxy.objects.wrappers.DatasetCollection method) (bioblend.galaxy.objects.wrappers.DatasetContainer method) (bioblend.galaxy.objects.wrappers.Folder method) reload() (bioblend.galaxy.tools.ToolClient method) reload_data_table() (bioblend.galaxy.tool_data.ToolDataClient method) reload_toolbox() (bioblend.galaxy.config.ConfigClient method) report_error() (bioblend.galaxy.jobs.JobsClient method) repository_revisions() (bioblend.toolshed.repositories.ToolShedRepositoryClient method)

requirements() (bioblend.galaxy.tools.ToolClient method) rerun_invocation() (bioblend.galaxy.invocations.InvocationClient method) rerun_job() (bioblend.galaxy.jobs.JobsClient method) resume_job() (bioblend.galaxy.jobs.JobsClient method) RolesClient (class in bioblend.galaxy.roles) root_folder (bioblend.galaxy.objects.wrappers.Library property) run() (bioblend.galaxy.objects.wrappers.Tool method) run_invocation_step_action() (bioblend.galaxy.invocations.InvocationClient method) (bioblend.galaxy.workflows.WorkflowClient method) run_tool() (bioblend.galaxy.tools.ToolClient method)

S

search_jobs() (bioblend.galaxy.jobs.JobsClient method) search_repositories() (bioblend.toolshed.repositories.ToolShedRepositoryClient method) search_tools() (bioblend.toolshed.tools.ToolShedToolClient method) set_dataset_permissions() (bioblend.galaxy.libraries.LibraryClient method) set_file_logger() (in module bioblend) set_library_permissions() (bioblend.galaxy.libraries.LibraryClient method) set_permissions() (bioblend.galaxy.folders.FoldersClient method) set_stream_logger() (in module bioblend) show_category() (bioblend.toolshed.categories.ToolShedCategoryClient method) show_data_table() (bioblend.galaxy.tool_data.ToolDataClient method) show_dataset() (bioblend.galaxy.datasets.DatasetClient method) (bioblend.galaxy.histories.HistoryClient method) (bioblend.galaxy.libraries.LibraryClient method) show_dataset_collection() (bioblend.galaxy.dataset_collections.DatasetCollectionClient method) (bioblend.galaxy.histories.HistoryClient method) show_dataset_provenance() (bioblend.galaxy.histories.HistoryClient method) show_folder() (bioblend.galaxy.folders.FoldersClient method) (bioblend.galaxy.libraries.LibraryClient method) show_form() (bioblend.galaxy.forms.FormsClient method) show_genome() (bioblend.galaxy.genomes.GenomeClient method) show_group() (bioblend.galaxy.groups.GroupsClient method) show_history() (bioblend.galaxy.histories.HistoryClient method) show_in_tool_panel (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) show_invocation() (bioblend.galaxy.invocations.InvocationClient method) (bioblend.galaxy.workflows.WorkflowClient method) show_invocation_step() (bioblend.galaxy.invocations.InvocationClient method) (bioblend.galaxy.workflows.WorkflowClient method)

show_job() (bioblend.galaxy.jobs.JobsClient method) show_job_lock() (bioblend.galaxy.jobs.JobsClient method) show_library() (bioblend.galaxy.libraries.LibraryClient method) show_matching_datasets() (bioblend.galaxy.histories.HistoryClient method) show_quota() (bioblend.galaxy.quotas.QuotaClient method) show_repository() (bioblend.galaxy.toolshed.ToolShedClient method) (bioblend.toolshed.repositories.ToolShedRepositoryClient method) show_repository_revision() (bioblend.toolshed.repositories.ToolShedRepositoryClient method) show_role() (bioblend.galaxy.roles.RolesClient method) show_tool() (bioblend.galaxy.tools.ToolClient method) show_user() (bioblend.galaxy.users.UserClient method) show_versions() (bioblend.galaxy.workflows.WorkflowClient method) show_visualization() (bioblend.galaxy.visual.VisualClient method) show_workflow() (bioblend.galaxy.workflows.WorkflowClient method) sink_ids (bioblend.galaxy.objects.wrappers.Workflow attribute) sorted_step_ids() (bioblend.galaxy.objects.wrappers.Workflow method) source_ids (bioblend.galaxy.objects.wrappers.Workflow attribute) SRC (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetCollectionAssociation attribute) (bioblend.galaxy.objects.wrappers.LibraryDataset attribute) (bioblend.galaxy.objects.wrappers.LibraryDatasetDatasetAssociation attribute) state (bioblend.galaxy.objects.wrappers.Dataset attribute) Step (class in bioblend.galaxy.objects.wrappers) steps (bioblend.galaxy.objects.wrappers.Workflow attribute) summarize_toolbox() (bioblend.galaxy.tool_dependencies.ToolDependenciesClient method) synopsis (bioblend.galaxy.objects.wrappers.Library attribute)

T

tags (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) TimeoutException to_dict() (bioblend.galaxy.dataset_collections.CollectionDescription method) (bioblend.galaxy.dataset_collections.CollectionElement method) to_json() (bioblend.galaxy.objects.wrappers.Wrapper method) Tool (class in bioblend.galaxy.objects.wrappers) tool_id (bioblend.galaxy.objects.wrappers.Step attribute) tool_ids (bioblend.galaxy.objects.wrappers.Workflow property) tool_inputs (bioblend.galaxy.objects.wrappers.Step attribute)

tool_labels_to_ids (bioblend.galaxy.objects.wrappers.Workflow attribute) tool_version (bioblend.galaxy.objects.wrappers.Step attribute) ToolClient (class in bioblend.galaxy.tools) ToolDataClient (class in bioblend.galaxy.tool_data) ToolDependenciesClient (class in bioblend.galaxy.tool_dependencies) ToolShedCategoryClient (class in bioblend.toolshed.categories) ToolShedClient (class in bioblend.galaxy.toolshed) ToolShedInstance (class in bioblend.toolshed) ToolShedRepositoryClient (class in bioblend.toolshed.repositories) ToolShedToolClient (class in bioblend.toolshed.tools) touch() (bioblend.galaxy.objects.wrappers.Wrapper method) type (bioblend.galaxy.objects.wrappers.Step attribute)

U

undelete_history() (bioblend.galaxy.histories.HistoryClient method) undelete_quota() (bioblend.galaxy.quotas.QuotaClient method) uninstall_dependencies() (bioblend.galaxy.tools.ToolClient method) uninstall_repository_revision() (bioblend.galaxy.toolshed.ToolShedClient method) unmap() (bioblend.galaxy.objects.wrappers.Wrapper method) unused_dependency_paths() (bioblend.galaxy.tool_dependencies.ToolDependenciesClient method) update() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation method) (bioblend.galaxy.objects.wrappers.LibraryDataset method) update_dataset() (bioblend.galaxy.histories.HistoryClient method) update_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) update_folder() (bioblend.galaxy.folders.FoldersClient method) update_group() (bioblend.galaxy.groups.GroupsClient method) update_history() (bioblend.galaxy.histories.HistoryClient method) update_job_lock() (bioblend.galaxy.jobs.JobsClient method) update_library_dataset() (bioblend.galaxy.libraries.LibraryClient method) update_permissions() (bioblend.galaxy.datasets.DatasetClient method) update_quota() (bioblend.galaxy.quotas.QuotaClient method) update_repository() (bioblend.toolshed.repositories.ToolShedRepositoryClient method)

update_repository_metadata() (bioblend.toolshed.repositories.ToolShedRepositoryClient method) update_user() (bioblend.galaxy.users.UserClient method) update_workflow() (bioblend.galaxy.workflows.WorkflowClient method) upload_data() (bioblend.galaxy.objects.wrappers.Library method) upload_dataset() (bioblend.galaxy.objects.wrappers.History method) upload_dataset_from_library() (bioblend.galaxy.histories.HistoryClient method) upload_file() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.tools.ToolClient method) upload_file_contents() (bioblend.galaxy.libraries.LibraryClient method) upload_file_from_local_path() (bioblend.galaxy.libraries.LibraryClient method) upload_file_from_server() (bioblend.galaxy.libraries.LibraryClient method) upload_file_from_url() (bioblend.galaxy.libraries.LibraryClient method) upload_from_ftp() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.tools.ToolClient method) upload_from_galaxy_filesystem() (bioblend.galaxy.libraries.LibraryClient method) upload_from_galaxy_fs() (bioblend.galaxy.objects.wrappers.Library method) upload_from_local() (bioblend.galaxy.objects.wrappers.Library method) upload_from_url() (bioblend.galaxy.objects.wrappers.Library method) UserClient (class in bioblend.galaxy.users)

V

VisualClient (class in bioblend.galaxy.visual)

W

wait() (bioblend.galaxy.objects.wrappers.Dataset method) wait_for_dataset() (bioblend.galaxy.datasets.DatasetClient method) (bioblend.galaxy.libraries.LibraryClient method) wait_for_dataset_collection() (bioblend.galaxy.dataset_collections.DatasetCollectionClient method) wait_for_invocation() (bioblend.galaxy.invocations.InvocationClient method) wait_for_job() (bioblend.galaxy.jobs.JobsClient method)

wait_on() (in module bioblend) whoami() (bioblend.galaxy.config.ConfigClient method) Workflow (class in bioblend.galaxy.objects.wrappers) WorkflowClient (class in bioblend.galaxy.workflows) WorkflowPreview (class in bioblend.galaxy.objects.wrappers) wrapped (bioblend.galaxy.objects.wrappers.Wrapper attribute) Wrapper (class in bioblend.galaxy.objects.wrappers)