• dataset_id (str) -- Encoded dataset ID
• file_path (str) -- If this argument is provided, the dataset will be streamed to disk at that path (should be a directory if use_default_filename=True). If the file_path argument is not provided, the dataset content is loaded into memory and returned by the method (Memory consumption may be heavy as the entire file will be in memory).
• use_default_filename (bool) -- If True, the exported file will be saved as file_path/%s, where %s is the dataset name. If False, file_path is assumed to contain the full file path including the filename.
• require_ok_state (bool) -- If False, datasets will be downloaded even if not in an 'ok' state, issuing a DatasetStateWarning rather than raising a DatasetStateException.
• maxwait (float) -- Total time (in seconds) to wait for the dataset state to become terminal. If the dataset state is not terminal within this time, a DatasetTimeoutException will be thrown.

• limit (int) -- Maximum number of datasets to return.
• offset (int) -- Return datasets starting from this specified position. For example, if limit is set to 100 and offset to 200, datasets 200-299 will be returned.
• name (str) -- Dataset name to filter on.
• extension (str or list of str) -- Dataset extension (or list of extensions) to filter on.
• state (str or list of str) -- Dataset state (or list of states) to filter on.
• visible (bool) -- Optionally filter datasets by their visible attribute.
• deleted (bool) -- Optionally filter datasets by their deleted attribute.
• purged (bool) -- Optionally filter datasets by their purged attribute.
• tool_id (str) -- Tool ID to filter on.
• tag (str) -- Dataset tag to filter on.
• history_id (str) -- Encoded history ID to filter on.
• create_time_min (str) -- Show only datasets created after the provided time and date, which should be formatted as YYYY-MM-DDTHH-MM-SS.
• create_time_max (str) -- Show only datasets created before the provided time and date, which should be formatted as YYYY-MM-DDTHH-MM-SS.
• update_time_min (str) -- Show only datasets last updated after the provided time and date, which should be formatted as YYYY-MM-DDTHH-MM-SS.
• update_time_max (str) -- Show only datasets last updated before the provided time and date, which should be formatted as YYYY-MM-DDTHH-MM-SS.
• order (str) -- One or more of the following attributes for ordering datasets: create_time (default), extension, hid, history_id, name, update_time. Optionally, -asc or -dsc (default) can be appended for ascending and descending order respectively. Multiple attributes can be stacked as a comma-separated list of values, e.g. create_time-asc,hid-dsc.

• dataset_id (str) -- dataset ID
• published (bool) -- Whether to make the dataset published (True) or private (False).

• dataset_id (str) -- Encoded dataset ID
• deleted (bool) -- Whether to return results for a deleted dataset
• hda_ldda (str) -- Whether to show a history dataset ('hda' - the default) or library dataset ('ldda').

• dataset_id (str) -- dataset ID
• access_ids (list) -- role IDs which should have access permissions for the dataset.
• manage_ids (list) -- role IDs which should have manage permissions for the dataset.
• modify_ids (list) -- role IDs which should have modify permissions for the dataset.

• dataset_id (str) -- dataset ID
• maxwait (float) -- Total time (in seconds) to wait for the dataset state to become terminal. If the dataset state is not terminal within this time, a DatasetTimeoutException will be raised.
• interval (float) -- Time (in seconds) to wait between 2 consecutive checks.
• check (bool) -- Whether to check if the dataset terminal state is 'ok'.

• dataset_collection_id (str) -- Encoded dataset collection ID
• file_path (str) -- The path to which the archive will be downloaded

• dataset_collection_id (str) -- dataset collection ID
• instance_type (str) -- instance type of the collection - 'history' or 'library'

• dataset_collection_id (str) -- dataset collection ID
• maxwait (float) -- Total time (in seconds) to wait for the dataset states in the dataset collection to become terminal. If not all datasets are in a terminal state within this time, a DatasetCollectionTimeoutException will be raised.
• interval (float) -- Time (in seconds) to wait between two consecutive checks.
• proportion_complete (float) -- Proportion of elements in this collection that have to be in a terminal state for this method to return. Must be a number between 0 and 1. For example: if the dataset collection contains 2 elements, and proportion_complete=0.5 is specified, then wait_for_dataset_collection will return as soon as 1 of the 2 datasets is in a terminal state. Default is 1, i.e. all elements must complete.
• check (bool) -- Whether to check if all the terminal states of datasets in the dataset collection are 'ok'. This will raise an Exception if a dataset is in a terminal state other than 'ok'.

• extension_only (bool) -- Return only the extension rather than the datatype name
• upload_only (bool) -- Whether to return only datatypes which can be uploaded

• parent_folder_id (str) -- Folder's description
• name (str) -- name of the new folder
• description (str) -- folder's description

• folder_id (str) -- the folder's encoded id, prefixed by 'F'
• undelete (bool) -- If set to True, the folder will be undeleted (i.e. the deleted mark will be removed)

• folder_id (str) -- the folder's encoded id, prefixed by 'F'
• scope (str) -- scope of permissions, either 'current' or 'available'

• folder_id (str) -- the folder's encoded id, prefixed by 'F'
• action (str) -- action to execute, only "set_permissions" is supported.
• add_ids (list of str) -- list of role IDs which can add datasets to the folder
• manage_ids (list of str) -- list of role IDs which can manage datasets in the folder
• modify_ids (list of str) -- list of role IDs which can modify datasets in the folder

• folder_id (str) -- the folder's encoded id, prefixed by 'F'
• contents (bool) -- True to get the contents of the folder, rather than just the folder details.

• folder_id (str) -- the folder's encoded id, prefixed by 'F'
• name (str) -- name of the new folder
• description (str) -- folder's description

• func (str) -- Allowed values: 'download', Download and index; 'index', Index only
• source (str) -- Data source for this build. Can be: UCSC, Ensembl, NCBI, URL
• dbkey (str) -- DB key of the build to download, ignored unless 'UCSC' is specified as the source
• ncbi_name (str) -- NCBI's genome identifier, ignored unless NCBI is specified as the source
• ensembl_dbkey (str) -- Ensembl's genome identifier, ignored unless Ensembl is specified as the source
• url_dbkey (str) -- DB key to use for this build, ignored unless URL is specified as the source
• indexers (list) -- POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...)

• id (str) -- Genome build ID to use
• num (str) -- num
• chrom (str) -- chrom
• low (str) -- low
• high (str) -- high

• group_id (str) -- Encoded group ID
• role_id (str) -- Encoded role ID to add to the group

• group_id (str) -- Encoded group ID
• user_id (str) -- Encoded user ID to add to the group

• group_name (str) -- A name for the new group
• user_ids (list) -- A list of encoded user IDs to add to the new group
• role_ids (list) -- A list of encoded role IDs to add to the new group

• group_id (str) -- Encoded group ID
• role_id (str) -- Encoded role ID to remove from the group

• group_id (str) -- Encoded group ID
• user_id (str) -- Encoded user ID to remove from the group

• group_id (str) -- Encoded group ID
• group_name (str) -- A new name for the group. If None, the group name is not changed.
• user_ids (list) -- New list of encoded user IDs for the group. It will substitute the previous list of users (with [] if not specified)
• role_ids (list) -- New list of encoded role IDs for the group. It will substitute the previous list of roles (with [] if not specified)

• history_id (str) -- ID of the history to which the content should be copied
• content_id (str) -- ID of the content to copy
• source (str) -- Source of the content to be copied: 'hda' (for a history dataset, the default), 'hdca' (for a dataset collection), 'library' (for a library dataset) or 'library_folder' (for all datasets in a library folder).

• history_id (str) -- history ID to which the dataset should be copied
• dataset_id (str) -- dataset ID
• source (str) -- Source of the dataset to be copied: 'hda' (the default), 'library' or 'library_folder'

• history_id (str) -- Encoded history ID
• collection_description (bioblend.galaxy.dataset_collections.CollectionDescription) --

  a description of the dataset collection For example:

{'collection_type': 'list',


 'element_identifiers': [{'id': 'f792763bee8d277a',


                          'name': 'element 1',


                          'src': 'hda'},


                         {'id': 'f792763bee8d277a',


                          'name': 'element 2',


                          'src': 'hda'}],


 'name': 'My collection list'}

• history_id (str) -- Encoded history ID
• tag (str) -- Add tag to history

• history_id (str) -- Encoded history ID
• dataset_id (str) -- Encoded dataset ID
• purge (bool) -- if True, also purge (permanently delete) the dataset

• history_id (str) -- Encoded history ID
• dataset_collection_id (str) -- Encoded dataset collection ID

• history_id (str) -- Encoded history ID
• purge (bool) -- if True, also purge (permanently delete) the history

• history_id (str) -- history ID
• jeha_id (str) -- jeha ID (this should be obtained via export_history())
• outf (file) -- output file object, open for writing in binary mode
• chunk_size (int) -- how many bytes at a time should be read into memory

• history_id (str) -- history ID
• gzip (bool) -- create .tar.gz archive if True, else .tar
• include_hidden (bool) -- whether to include hidden datasets in the export
• include_deleted (bool) -- whether to include deleted datasets in the export
• wait (bool) -- if True, block until the export is ready; else, return immediately
• maxwait (float) -- Total time (in seconds) to wait for the export to become ready. When set, implies that wait is True.

• history_id (str) -- history ID
• dataset_id (str) -- dataset ID

• name (str) -- History name to filter on.
• deleted (bool) -- whether to filter for the deleted histories (True) or for the non-deleted ones (False)
• published (bool or None) -- whether to filter for the published histories (True) or for the non-published ones (False). If not set, no filtering is applied. Note the filtering is only applied to the user's own histories; to access all histories published by any user, use the get_published_histories method.
• slug (str) -- History slug to filter on
• all (bool) -- Whether to include histories from other users. This parameter works only on Galaxy 20.01 or later and can be specified only if the user is a Galaxy admin.

• name (str) -- History name to filter on.
• deleted (bool) -- whether to filter for the deleted histories (True) or for the non-deleted ones (False)
• slug (str) -- History slug to filter on

• file_path (str) -- Path to exported history archive on disk.
• url (str) -- URL for an exported history archive

• history_id (str) -- Encoded history ID
• dataset_id (str) -- Encoded dataset ID

• history_id (str) -- Encoded history ID
• dataset_collection_id (str) -- Encoded dataset collection ID

• history_id (str) -- Encoded history ID
• dataset_id (str) -- Encoded dataset ID
• follow (bool) -- If True, recursively fetch dataset provenance information for all inputs and their inputs, etc.

• history_id (str) -- Encoded history ID to filter on
• contents (bool) -- When True, instead of the history details, return a list with info for all datasets in the given history. Note that inside each dataset info dict, the id which should be used for further requests about this history dataset is given by the value of the id (not dataset_id) key.
• deleted (bool or None) -- When contents=True, whether to filter for the deleted datasets (True) or for the non-deleted ones (False). If not set, no filtering is applied.
• visible (bool or None) -- When contents=True, whether to filter for the visible datasets (True) or for the hidden ones (False). If not set, no filtering is applied.
• details (str) -- When contents=True, include dataset details. Set to 'all' for the most information.
• types (list) -- When contents=True, filter for history content types. If set to ['dataset'], return only datasets. If set to ['dataset_collection'], return only dataset collections. If not set, no filtering is applied.

• history_id (str) -- Encoded history ID
• name_filter (str) -- Only datasets whose name matches the name_filter regular expression will be returned; use plain strings for exact matches and None to match all datasets in the history

• history_id (str) -- Encoded history ID
• dataset_id (str) -- ID of the dataset
• name (str) -- Replace history dataset name with the given string
• datatype (str) -- Replace the datatype of the history dataset with the given string. The string must be a valid Galaxy datatype, both the current and the target datatypes must allow datatype changes, and the dataset must not be in use as input or output of a running job (including uploads), otherwise an error will be raised.
• genome_build (str) -- Replace history dataset genome build (dbkey)
• annotation (str) -- Replace history dataset annotation with given string
• deleted (bool) -- Mark or unmark history dataset as deleted
• visible (bool) -- Mark or unmark history dataset as visible

• history_id (str) -- Encoded history ID
• dataset_collection_id (str) -- Encoded dataset_collection ID
• name (str) -- Replace history dataset collection name with the given string
• deleted (bool) -- Mark or unmark history dataset collection as deleted
• visible (bool) -- Mark or unmark history dataset collection as visible

• history_id (str) -- Encoded history ID
• name (str) -- Replace history name with the given string
• annotation (str) -- Replace history annotation with given string
• deleted (bool) -- Mark or unmark history as deleted
• purged (bool) -- If True, mark history as purged (permanently deleted).
• published (bool) -- Mark or unmark history as published
• importable (bool) -- Mark or unmark history as importable
• tags (list) -- Replace history tags with the given list

• history_id (str) -- Encoded history ID
• lib_dataset_id (str) -- Encoded library dataset ID

• invocation_id (str) -- Encoded workflow invocation ID
• file_path (str) -- Path to save the report

• workflow_id (str) -- Encoded workflow ID to filter on
• history_id (str) -- Encoded history ID to filter on
• user_id (str) -- Encoded user ID to filter on. This must be your own user ID if your are not an admin user.
• include_terminal (bool) -- Whether to include terminal states.
• limit (int) -- Maximum number of invocations to return - if specified, the most recent invocations will be returned.
• view (str) -- Level of detail to return per invocation, either 'element' or 'collection'.
• step_details (bool) -- If 'view' is 'element', also include details on individual steps.

• invocation_id (str) -- Encoded workflow invocation ID to be rerun
• inputs_update (dict) -- If different datasets should be used to the original invocation, this should contain a mapping of workflow inputs to the new datasets and dataset collections.
• params_update (dict) -- If different non-dataset tool parameters should be used to the original invocation, this should contain a mapping of the new parameter values.
• history_id (str) -- The encoded history ID where to store the workflow outputs. Alternatively, history_name may be specified to create a new history.
• history_name (str) -- Create a new history with the given name to store the workflow outputs. If both history_id and history_name are provided, history_name is ignored. If neither is specified, a new 'Unnamed history' is created.
• import_inputs_to_history (bool) -- If True, used workflow inputs will be imported into the history. If False, only workflow outputs will be visible in the given history.
• allow_tool_state_corrections (bool) -- If True, allow Galaxy to fill in missing tool state when running workflows. This may be useful for workflows using tools that have changed over time or for workflows built outside of Galaxy with only a subset of inputs defined.
• replacement_params (dict) -- pattern-based replacements for post-job actions
• inputs_by (str) -- Determines how inputs are referenced. Can be "step_index|step_uuid" (default), "step_index", "step_id", "step_uuid", or "name".
• parameters_normalized (bool) -- Whether Galaxy should normalize the input parameters to ensure everything is referenced by a numeric step ID. Default is False, but when setting parameters for a subworkflow, True is required.

• invocation_id (str) -- Encoded workflow invocation ID
• step_id (str) -- Encoded workflow invocation step ID
• action (object) -- Action to use when updating state, semantics depends on step type.

• invocation_id (str) -- Encoded workflow invocation ID
• step_id (str) -- Encoded workflow invocation step ID

• invocation_id (str) -- Invocation ID to wait for.
• maxwait (float) -- Total time (in seconds) to wait for the invocation state to become terminal. If the invocation state is not terminal within this time, a TimeoutException will be raised.
• interval (float) -- Time (in seconds) to wait between 2 consecutive checks.
• check (bool) -- Whether to check if the invocation terminal state is 'scheduled'.

• state (str or list of str) -- Job states to filter on.
• history_id (str) -- Encoded history ID to filter on.
• invocation_id (string) -- Encoded workflow invocation ID to filter on.
• tool_id (str or list of str) -- Tool IDs to filter on.
• workflow_id (string) -- Encoded workflow ID to filter on.
• user_id (str) -- Encoded user ID to filter on. Only admin users can access the jobs of other users.
• date_range_min (str) -- Mininum job update date (in YYYY-MM-DD format) to filter on.
• date_range_max (str) -- Maximum job update date (in YYYY-MM-DD format) to filter on.
• limit (int) -- Maximum number of jobs to return.
• offset (int) -- Return jobs starting from this specified position. For example, if limit is set to 100 and offset to 200, jobs 200-299 will be returned.
• user_details (bool) -- If True and the user is an admin, add the user email to each returned job dictionary.
• order_by (str) -- Whether to order jobs by create_time or update_time (the default).

• job_id (str) -- job ID
• dataset_id (str) -- Dataset ID
• message (str) -- Error message
• email (str) -- Email for error report submission. If not specified, the email associated with the Galaxy user account is used by default.

• job_id (str) -- job ID
• remap (bool) -- when True, the job output(s) will be remapped onto the dataset(s) created by the original job; if other jobs were waiting for this job to finish successfully, they will be resumed using the new outputs of this tool run. When False, new job output(s) will be created. Note that if Galaxy does not permit remapping for the job in question, specifying True will result in an error.
• tool_inputs_update (dict) -- dictionary specifying any changes which should be made to tool parameters for the rerun job. This dictionary should have the same structure as is required when submitting the tool_inputs dictionary to gi.tools.run_tool(), but only needs to include the inputs or parameters to be updated for the rerun job.
• history_id (str) -- ID of the history in which the job should be executed; if not specified, the same history will be used as the original job run.

• tool_id (str) -- only return jobs associated with this tool ID
• inputs (dict) -- return only jobs that have matching inputs
• state (str) -- only return jobs in this state

• job_id (str) -- job ID
• full_details (bool) -- when True, the complete list of details for the given job.

• job_id (str) -- job ID
• maxwait (float) -- Total time (in seconds) to wait for the job state to become terminal. If the job state is not terminal within this time, a TimeoutException will be raised.
• interval (float) -- Time (in seconds) to wait between 2 consecutive checks.
• check (bool) -- Whether to check if the job terminal state is 'ok'.

• library_id (str) -- id of the library where to place the uploaded file
• dataset_id (str) -- id of the dataset to copy from
• folder_id (str) -- id of the folder where to place the uploaded files. If not provided, the root folder will be used
• message (str) -- message for copying action

• library_id (str) -- library id to use
• folder_name (str) -- name of the new folder in the data library
• description (str) -- description of the new folder in the data library
• base_folder_id (str) -- id of the folder where to create the new folder. If not provided, the root folder will be used

• name (str) -- Name of the new data library
• description (str) -- Optional data library description
• synopsis (str) -- Optional data library synopsis

• library_id (str) -- library id where dataset is found in
• dataset_id (str) -- id of the dataset to be deleted
• purged (bool) -- Indicate that the dataset should be purged (permanently deleted)

• library_id (str) -- library id to use
• name (str) -- Folder name to filter on. For name specify the full path of the folder starting from the library's root folder, e.g. /subfolder/subsubfolder.

• name (str) -- Library name to filter on.
• deleted (bool) -- If False (the default), return only non-deleted libraries. If True, return only deleted libraries. If None, return both deleted and non-deleted libraries.

• dataset_id (str) -- id of the dataset
• access_in (list) -- list of role ids
• modify_in (list) -- list of role ids
• manage_in (list) -- list of role ids

• library_id (str) -- id of the library
• access_in (list) -- list of role ids
• modify_in (list) -- list of role ids
• add_in (list) -- list of role ids
• manage_in (list) -- list of role ids

• library_id (str) -- library id where dataset is found in
• dataset_id (str) -- id of the dataset to be inspected

• library_id (str) -- library id to inspect folders in
• folder_id (str) -- id of the folder to be inspected

• library_id (str) -- filter for library by library id
• contents (bool) -- whether to get contents of the library (rather than just the library details)

• dataset_id (str) -- id of the dataset to be updated
• name (str) -- Replace library dataset name with the given string
• misc_info (str) -- Replace library dataset misc_info with given string
• file_ext (str) -- Replace library dataset extension (must exist in the Galaxy registry)
• genome_build (str) -- Replace library dataset genome build (dbkey)
• tags (list) -- Replace library dataset tags with the given list

• library_id (str) -- id of the library where to place the uploaded file
• pasted_content (str) -- Content to upload into the library
• folder_id (str) -- id of the folder where to place the uploaded file. If not provided, the root folder will be used
• file_type (str) -- Galaxy file format name
• dbkey (str) -- Dbkey
• tags (list) -- A list of tags to add to the datasets

• library_id (str) -- id of the library where to place the uploaded file
• file_local_path (str) -- path of local file to upload
• folder_id (str) -- id of the folder where to place the uploaded file. If not provided, the root folder will be used
• file_type (str) -- Galaxy file format name
• dbkey (str) -- Dbkey
• tags (list) -- A list of tags to add to the datasets

• library_id (str) -- id of the library where to place the uploaded file
• server_dir (str) -- relative path of the subdirectory of library_import_dir to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded
• folder_id (str) -- id of the folder where to place the uploaded files. If not provided, the root folder will be used
• file_type (str) -- Galaxy file format name
• dbkey (str) -- Dbkey
• link_data_only (str) -- either 'copy_files' (default) or 'link_to_files'. Setting to 'link_to_files' symlinks instead of copying the files
• roles (str) --

  ???

• preserve_dirs (bool) -- Indicate whether to preserve the directory structure when importing dir
• tag_using_filenames (bool) --

  Indicate whether to generate dataset tags from filenames.

  Changed in version 0.14.0: Changed the default from True to False.

• tags (list) -- A list of tags to add to the datasets

• library_id (str) -- id of the library where to place the uploaded file
• file_url (str) -- URL of the file to upload
• folder_id (str) -- id of the folder where to place the uploaded file. If not provided, the root folder will be used
• file_type (str) -- Galaxy file format name
• dbkey (str) -- Dbkey
• tags (list) -- A list of tags to add to the datasets

• library_id (str) -- id of the library where to place the uploaded file
• filesystem_paths (str) -- file paths on the Galaxy server to upload to the library, one file per line
• folder_id (str) -- id of the folder where to place the uploaded files. If not provided, the root folder will be used
• file_type (str) -- Galaxy file format name
• dbkey (str) -- Dbkey
• link_data_only (str) -- either 'copy_files' (default) or 'link_to_files'. Setting to 'link_to_files' symlinks instead of copying the files
• roles (str) --

  ???

• preserve_dirs (bool) -- Indicate whether to preserve the directory structure when importing dir
• tag_using_filenames (bool) --

  Indicate whether to generate dataset tags from filenames.

  Changed in version 0.14.0: Changed the default from True to False.

• tags (list) -- A list of tags to add to the datasets

• library_id (str) -- library id where dataset is found in
• dataset_id (str) -- id of the dataset to wait for
• maxwait (float) -- Total time (in seconds) to wait for the dataset state to become terminal. If the dataset state is not terminal within this time, a DatasetTimeoutException will be thrown.
• interval (float) -- Time (in seconds) to wait between 2 consecutive checks.

• name (str) -- Name for the new quota. This must be unique within a Galaxy instance.
• description (str) -- Quota description
• amount (str) -- Quota size (E.g. 10000MB, 99 gb, 0.2T, unlimited)
• operation (str) -- One of (+, -, =)
• default (str) -- Whether or not this is a default quota. Valid values are no, unregistered, registered. None is equivalent to no.
• in_users (list of str) -- A list of user IDs or user emails.
• in_groups (list of str) -- A list of group IDs or names.

• quota_id (str) -- Encoded quota ID
• deleted (bool) -- Search for quota in list of ones already marked as deleted

• quota_id (str) -- Encoded quota ID
• name (str) -- Name for the new quota. This must be unique within a Galaxy instance.
• description (str) -- Quota description. If you supply this parameter, but not the name, an error will be thrown.
• amount (str) -- Quota size (E.g. 10000MB, 99 gb, 0.2T, unlimited)
• operation (str) -- One of (+, -, =). If you wish to change this value, you must also provide the amount, otherwise it will not take effect.
• default (str) -- Whether or not this is a default quota. Valid values are no, unregistered, registered. Calling this method with default="no" on a non-default quota will throw an error. Not passing this parameter is equivalent to passing no.
• in_users (list of str) -- A list of user IDs or user emails.
• in_groups (list of str) -- A list of group IDs or names.

• role_name (str) -- A name for the new role
• description (str) -- Description for the new role
• user_ids (list) -- A list of encoded user IDs to add to the new role
• group_ids (list) -- A list of encoded group IDs to add to the new role

• data_table_id (str) -- ID of the data table
• values (str) -- a "|" separated list of column contents, there must be a value for all the columns of the data table

• index (int) -- index of the dependency resolver with respect to the dependency resolvers config file
• tool_ids (list) -- tool_ids to return when index_by=tools
• resolver_type (str) -- restrict to specified resolver type
• include_containers (bool) -- include container resolvers in resolution
• container_type (str) -- restrict to specified container type
• index_by (str) -- By default results are grouped by requirements. Set to 'tools' to return one entry per tool.

• workflow_id (str) -- Encoded workflow ID
• invocation_id (str) -- Encoded workflow invocation ID

• workflow_id (str) -- Encoded workflow ID
• version (int) -- Workflow version to export

• workflow_id (str) -- Encoded workflow ID
• file_local_path (str) -- Local path to which the exported file will be saved. (Should not contain filename if use_default_name=True)
• use_default_filename (bool) -- If the use_default_name parameter is True, the exported file will be saved as file_local_path/Galaxy-Workflow-%s.ga, where %s is the workflow name. If use_default_name is False, file_local_path is assumed to contain the full file path including filename.

• history_id (str) -- Encoded history ID
• workflow_name (str) -- Name of the workflow to create
• job_ids (list) -- Optional list of job IDs to filter the jobs to extract from the history
• dataset_hids (list) -- Optional list of dataset hids corresponding to workflow inputs when extracting a workflow from history
• dataset_collection_hids (list) -- Optional list of dataset collection hids corresponding to workflow inputs when extracting a workflow from history

• workflow_id (str) -- Encoded workflow ID
• label (str) -- label to filter workflow inputs on

• name (str) -- Workflow name to filter on.
• published (bool) -- if True, return also published workflows

• workflow_dict (dict) -- dictionary representing the workflow to be imported
• publish (bool) -- if True the uploaded workflow will be published; otherwise it will be visible only by the user which uploads it (default)

• file_local_path (str) -- File to upload to the server for new workflow
• publish (bool) -- if True the uploaded workflow will be published; otherwise it will be visible only by the user which uploads it (default)

• workflow_id (str) -- Encoded workflow ID
• inputs (dict) --

  A mapping of workflow inputs to datasets and dataset collections. The datasets source can be a LibraryDatasetDatasetAssociation (ldda), LibraryDataset (ld), HistoryDatasetAssociation (hda), or HistoryDatasetCollectionAssociation (hdca).

  The map must be in the following format: {'<input_index>': {'id': <encoded dataset ID>, 'src': '[ldda, ld, hda, hdca]'}} (e.g. {'2': {'id': '29beef4fadeed09f', 'src': 'hda'}})

  This map may also be indexed by the UUIDs of the workflow steps, as indicated by the uuid property of steps returned from the Galaxy API. Alternatively workflow steps may be addressed by the label that can be set in the workflow editor. If using uuid or label you need to also set the inputs_by parameter to step_uuid or name.

• params (dict) -- A mapping of non-datasets tool parameters (see below)
• history_id (str) -- The encoded history ID where to store the workflow output. Alternatively, history_name may be specified to create a new history.
• history_name (str) -- Create a new history with the given name to store the workflow output. If both history_id and history_name are provided, history_name is ignored. If neither is specified, a new 'Unnamed history' is created.
• import_inputs_to_history (bool) -- If True, used workflow inputs will be imported into the history. If False, only workflow outputs will be visible in the given history.
• allow_tool_state_corrections (bool) -- If True, allow Galaxy to fill in missing tool state when running workflows. This may be useful for workflows using tools that have changed over time or for workflows built outside of Galaxy with only a subset of inputs defined.
• replacement_params (dict) -- pattern-based replacements for post-job actions (see below)
• inputs_by (str) -- Determines how inputs are referenced. Can be "step_index|step_uuid" (default), "step_index", "step_id", "step_uuid", or "name".
• parameters_normalized (bool) -- Whether Galaxy should normalize params to ensure everything is referenced by a numeric step ID. Default is False, but when setting params for a subworkflow, True is required.
• require_exact_tool_versions (bool) -- Whether invocation should fail if Galaxy does not have the exact tool versions. Default is True. Parameter does not any effect for Galaxy versions < 22.05.

{STEP_ID: PARAM_DICT, ...}

{PARAM_NAME: VALUE, ...}

{TOOL_ID: PARAM_DICT, ...}

{'param': PARAM_NAME, 'value': VALUE}

<repeat name="cutoff" title="Parameters used to filter cells" min="1">


    <param name="name" type="text" value="n_genes" label="Name of param...">


        <option value="n_genes">n_genes</option>


        <option value="n_counts">n_counts</option>


    </param>


    <param name="min" type="float" min="0" value="0" label="Min value"/>
</repeat>

{...


 "cutoff_0|name": "n_genes",


 "cutoff_0|min": "2",


 "cutoff_1|name": "n_counts",


 "cutoff_1|min": "4",


 ...}

{'RenameDatasetActionout_file1': {'action_arguments': {'newname': '${output}'},


                                  'action_type': 'RenameDatasetAction',


                                  'output_name': 'out_file1'}}

replacement_params = {'output': 'foo'}

• workflow_id (str) -- Encoded workflow ID
• actions (list of dicts) -- .INDENT 2.0

Actions to use for refactoring the workflow. The following

actions are supported: update_step_label, update_step_position, update_output_label, update_name, update_annotation, update_license, update_creator, update_report, add_step, add_input, disconnect, connect, fill_defaults, fill_step_defaults, extract_input, extract_legacy_parameter, remove_unlabeled_workflow_outputs, upgrade_all_steps, upgrade_subworkflow, upgrade_tool.

{'history_id': '2f94e8ae9edff68a',


 'id': 'df7a1f0c02a5b08e',


 'inputs': {'0': {'id': 'a7db2fac67043c7e',


                  'src': 'hda',


                  'uuid': '7932ffe0-2340-4952-8857-dbaa50f1f46a'}},


 'model_class': 'WorkflowInvocation',


 'state': 'ready',


 'steps': [{'action': None,


            'id': 'd413a19dec13d11e',


            'job_id': None,


            'model_class': 'WorkflowInvocationStep',


            'order_index': 0,


            'state': None,


            'update_time': '2015-10-31T22:00:26',


            'workflow_step_id': 'cbbbf59e8f08c98c',


            'workflow_step_label': None,


            'workflow_step_uuid': 'b81250fd-3278-4e6a-b269-56a1f01ef485'},


           {'action': None,


            'id': '2f94e8ae9edff68a',


            'job_id': 'e89067bb68bee7a0',


            'model_class': 'WorkflowInvocationStep',


            'order_index': 1,


            'state': 'new',


            'update_time': '2015-10-31T22:00:26',


            'workflow_step_id': '964b37715ec9bd22',


            'workflow_step_label': None,


            'workflow_step_uuid': 'e62440b8-e911-408b-b124-e05435d3125e'}],


 'update_time': '2015-10-31T22:00:26',


 'uuid': 'c8aa2b1c-801a-11e5-a9e5-8ca98228593c',


 'workflow_id': '03501d7626bd192f'}

{'action': None,


 'id': '63cd3858d057a6d1',


 'job_id': None,


 'model_class': 'WorkflowInvocationStep',


 'order_index': 2,


 'state': None,


 'update_time': '2015-10-31T22:11:14',


 'workflow_step_id': '52e496b945151ee8',


 'workflow_step_label': None,


 'workflow_step_uuid': '4060554c-1dd5-4287-9040-8b4f281cf9dc'}

{'id': '92c56938c2f9b315',


 'inputs': {'23': {'label': 'Input Dataset', 'value': ''}},


 'name': 'Simple',


 'url': '/api/workflows/92c56938c2f9b315'}