workflows¶
This section is auto-generated from the help text for the parsec command
workflows
.
cancel_invocation
command¶
Usage:
parsec workflows cancel_invocation [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
Cancel the scheduling of a workflow.
Output
Options:
-h, --help Show this message and exit.
delete_workflow
command¶
Usage:
parsec workflows delete_workflow [OPTIONS] WORKFLOW_ID
Help
Delete a workflow identified by workflow_id.
Output
Options:
-h, --help Show this message and exit.
export_workflow_dict
command¶
Usage:
parsec workflows export_workflow_dict [OPTIONS] WORKFLOW_ID
Help
Exports a workflow.
Output
Dictionary representing the requested workflow
Options:
-h, --help Show this message and exit.
export_workflow_json
command¶
Usage:
parsec workflows export_workflow_json [OPTIONS] WORKFLOW_ID
Help
Deprecated since version 0.9.0: Use export_workflow_dict()
instead.
Output
Options:
-h, --help Show this message and exit.
export_workflow_to_local_path
command¶
Usage:
parsec workflows export_workflow_to_local_path [OPTIONS] WORKFLOW_ID
Help
Exports a workflow in JSON format to a given local path.
Output
Options:
--use_default_filename 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.
[default: True]
-h, --help Show this message and exit.
get_invocations
command¶
Usage:
parsec workflows get_invocations [OPTIONS] WORKFLOW_ID
Help
Get a list containing all the workflow invocations corresponding to the specified workflow.
Output
- A list of workflow invocations.
For example:
[{u'history_id': u'2f94e8ae9edff68a', u'id': u'df7a1f0c02a5b08e', u'model_class': u'WorkflowInvocation', u'state': u'new', u'update_time': u'2015-10-31T22:00:22', u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c', u'workflow_id': u'03501d7626bd192f'}]
Options:
-h, --help Show this message and exit.
get_workflow_inputs
command¶
Usage:
parsec workflows get_workflow_inputs [OPTIONS] WORKFLOW_ID LABEL
Help
Get a list of workflow input IDs that match the given label. If no input matches the given label, an empty list is returned.
Output
list of workflow inputs matching the label query
Options:
-h, --help Show this message and exit.
get_workflows
command¶
Usage:
parsec workflows get_workflows [OPTIONS]
Help
Get all workflows or filter the specific one(s) via the provided name
or workflow_id
. Provide only one argument, name
or workflow_id
, but not both.
Output
- A list of workflow dicts.
For example:
[{u'id': u'92c56938c2f9b315', u'name': u'Simple', u'url': u'/api/workflows/92c56938c2f9b315'}]
Options:
--workflow_id TEXT Encoded workflow ID (incompatible with ``name``)
--name TEXT Filter by name of workflow (incompatible with
``workflow_id``). If multiple names match the given name,
all the workflows matching the argument will be returned.
--published if ``True``, return also published workflows
-h, --help Show this message and exit.
import_workflow_dict
command¶
Usage:
parsec workflows import_workflow_dict [OPTIONS] WORKFLOW_DICT
Help
Imports a new workflow given a dictionary representing a previously exported workflow.
Output
Options:
--publish if ``True`` the uploaded workflow will be published; otherwise it
will be visible only by the user which uploads it (default)
-h, --help Show this message and exit.
import_workflow_from_local_path
command¶
Usage:
parsec workflows import_workflow_from_local_path [OPTIONS]
Help
Imports a new workflow given the path to a file containing a previously exported workflow.
Output
Options:
--publish if ``True`` the uploaded workflow will be published; otherwise it
will be visible only by the user which uploads it (default)
-h, --help Show this message and exit.
import_workflow_json
command¶
Usage:
parsec workflows import_workflow_json [OPTIONS] WORKFLOW_JSON
Help
Deprecated since version 0.9.0: Use import_workflow_dict()
instead.
Output
Options:
-h, --help Show this message and exit.
invoke_workflow
command¶
Usage:
parsec workflows invoke_workflow [OPTIONS] WORKFLOW_ID
Help
Invoke the workflow identified by workflow_id
. This will cause a workflow to be scheduled and return an object describing the workflow invocation.
Output
- A dict containing the workflow invocation describing the
scheduling of the workflow. For example:
{u'history_id': u'2f94e8ae9edff68a', u'id': u'df7a1f0c02a5b08e', u'inputs': {u'0': {u'id': u'a7db2fac67043c7e', u'src': u'hda', u'uuid': u'7932ffe0-2340-4952-8857-dbaa50f1f46a'}}, u'model_class': u'WorkflowInvocation', u'state': u'ready', u'steps': [{u'action': None, u'id': u'd413a19dec13d11e', u'job_id': None, u'model_class': u'WorkflowInvocationStep', u'order_index': 0, u'state': None, u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'cbbbf59e8f08c98c', u'workflow_step_label': None, u'workflow_step_uuid': u'b81250fd-3278-4e6a-b269-56a1f01ef485'}, {u'action': None, u'id': u'2f94e8ae9edff68a', u'job_id': u'e89067bb68bee7a0', u'model_class': u'WorkflowInvocationStep', u'order_index': 1, u'state': u'new', u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'964b37715ec9bd22', u'workflow_step_label': None, u'workflow_step_uuid': u'e62440b8-e911-408b-b124-e05435d3125e'}], u'update_time': u'2015-10-31T22:00:26', u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c', u'workflow_id': u'03501d7626bd192f'}The
params
dict should be specified as follows:{STEP_ID: PARAM_DICT, ...}where PARAM_DICT is:
{PARAM_NAME: VALUE, ...}For backwards compatibility, the following (deprecated) format is also supported for
params
:{TOOL_ID: PARAM_DICT, ...}in which case PARAM_DICT affects all steps with the given tool id. If both by-tool-id and by-step-id specifications are used, the latter takes precedence.
Finally (again, for backwards compatibility), PARAM_DICT can also be specified as:
{'param': PARAM_NAME, 'value': VALUE}Note that this format allows only one parameter to be set per step.
The
replacement_params
dict should map parameter names in post-job actions (PJAs) to their runtime values. For instance, if the final step has a PJA like the following:{u'RenameDatasetActionout_file1': {u'action_arguments': {u'newname': u'${output}'}, u'action_type': u'RenameDatasetAction', u'output_name': u'out_file1'}}then the following renames the output dataset to ‘foo’:
replacement_params = {'output': 'foo'}see also this email thread.
Warning
Historically, the
run_workflow
method consumed adataset_map
data structure that was indexed by unencoded workflow step IDs. These IDs would not be stable across Galaxy instances. The newinputs
property is instead indexed by either theorder_index
property (which is stable across workflow imports) or the step UUID which is also stable.
Options:
--inputs TEXT 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``).
--params TEXT A mapping of non-datasets tool parameters (see
below)
--history_id TEXT The encoded history ID where to store the
workflow output. Alternatively,
``history_name`` may be specified to create a
new history.
--history_name TEXT 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 If ``True``, used workflow inputs will be
imported into the history. If ``False``, only
workflow outputs will be visible in the given
history.
--replacement_params TEXT pattern-based replacements for post-job
actions (see below)
--allow_tool_state_corrections 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.
-h, --help Show this message and exit.
run_invocation_step_action
command¶
Usage:
parsec workflows run_invocation_step_action [OPTIONS] WORKFLOW_ID
Help
nature of this action and what is expected will vary based on the the type of workflow step (the only currently valid action is True/False for pause steps).
Output
Options:
-h, --help Show this message and exit.
run_workflow
command¶
Usage:
parsec workflows run_workflow [OPTIONS] WORKFLOW_ID
Help
Run the workflow identified by workflow_id
.
Output
- A dict containing the history ID where the outputs are placed
as well as output dataset IDs. For example:
{u'history': u'64177123325c9cfd', u'outputs': [u'aa4d3084af404259']}The
params
dict should be specified as follows:{STEP_ID: PARAM_DICT, ...}where PARAM_DICT is:
{PARAM_NAME: VALUE, ...}For backwards compatibility, the following (deprecated) format is also supported for
params
:{TOOL_ID: PARAM_DICT, ...}in which case PARAM_DICT affects all steps with the given tool id. If both by-tool-id and by-step-id specifications are used, the latter takes precedence.
Finally (again, for backwards compatibility), PARAM_DICT can also be specified as:
{'param': PARAM_NAME, 'value': VALUE}Note that this format allows only one parameter to be set per step.
The
replacement_params
dict should map parameter names in post-job actions (PJAs) to their runtime values. For instance, if the final step has a PJA like the following:{u'RenameDatasetActionout_file1': {u'action_arguments': {u'newname': u'${output}'}, u'action_type': u'RenameDatasetAction', u'output_name': u'out_file1'}}then the following renames the output dataset to ‘foo’:
replacement_params = {'output': 'foo'}see also this email thread.
Warning
This method waits for the whole workflow to be scheduled before returning and does not scale to large workflows as a result. This method has therefore been deprecated in favor of
invoke_workflow()
, which also features improved default behavior for dataset input handling.
Options:
--dataset_map TEXT A mapping of workflow inputs to datasets. The
datasets source can be a
LibraryDatasetDatasetAssociation (``ldda``),
LibraryDataset (``ld``), or
HistoryDatasetAssociation (``hda``). The map must
be in the following format: ``{'<input>': {'id':
<encoded dataset ID>, 'src': '[ldda, ld, hda]'}}``
(e.g. ``{'23': {'id': '29beef4fadeed09f', 'src':
'ld'}}``)
--params TEXT A mapping of non-datasets tool parameters (see
below)
--history_id TEXT The encoded history ID where to store the workflow
output. Alternatively, ``history_name`` may be
specified to create a new history.
--history_name TEXT 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 If ``True``, used workflow inputs will be imported
into the history. If ``False``, only workflow
outputs will be visible in the given history.
--replacement_params TEXT pattern-based replacements for post-job actions
(see below)
-h, --help Show this message and exit.
show_invocation
command¶
Usage:
parsec workflows show_invocation [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
Get a workflow invocation object representing the scheduling of a workflow. This object may be sparse at first (missing inputs and invocation steps) and will become more populated as the workflow is actually scheduled.
Output
- The workflow invocation.
For example:
{u'history_id': u'2f94e8ae9edff68a', u'id': u'df7a1f0c02a5b08e', u'inputs': {u'0': {u'id': u'a7db2fac67043c7e', u'src': u'hda', u'uuid': u'7932ffe0-2340-4952-8857-dbaa50f1f46a'}}, u'model_class': u'WorkflowInvocation', u'state': u'ready', u'steps': [{u'action': None, u'id': u'd413a19dec13d11e', u'job_id': None, u'model_class': u'WorkflowInvocationStep', u'order_index': 0, u'state': None, u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'cbbbf59e8f08c98c', u'workflow_step_label': None, u'workflow_step_uuid': u'b81250fd-3278-4e6a-b269-56a1f01ef485'}, {u'action': None, u'id': u'2f94e8ae9edff68a', u'job_id': u'e89067bb68bee7a0', u'model_class': u'WorkflowInvocationStep', u'order_index': 1, u'state': u'new', u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'964b37715ec9bd22', u'workflow_step_label': None, u'workflow_step_uuid': u'e62440b8-e911-408b-b124-e05435d3125e'}], u'update_time': u'2015-10-31T22:00:26', u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c', u'workflow_id': u'03501d7626bd192f'}
Options:
-h, --help Show this message and exit.
show_invocation_step
command¶
Usage:
parsec workflows show_invocation_step [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
See the details of a particular workflow invocation step.
Output
- The workflow invocation step.
For example:
{u'action': None, u'id': u'63cd3858d057a6d1', u'job_id': None, u'model_class': u'WorkflowInvocationStep', u'order_index': 2, u'state': None, u'update_time': u'2015-10-31T22:11:14', u'workflow_step_id': u'52e496b945151ee8', u'workflow_step_label': None, u'workflow_step_uuid': u'4060554c-1dd5-4287-9040-8b4f281cf9dc'}
Options:
-h, --help Show this message and exit.
show_workflow
command¶
Usage:
parsec workflows show_workflow [OPTIONS] WORKFLOW_ID
Help
Display information needed to run a workflow.
Output
- A description of the workflow and its inputs.
For example:
{u'id': u'92c56938c2f9b315', u'inputs': {u'23': {u'label': u'Input Dataset', u'value': u''}}, u'name': u'Simple', u'url': u'/api/workflows/92c56938c2f9b315'}
Options:
-h, --help Show this message and exit.