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This represents a non-input step a Galaxy Workflow.

A note about state and tool_state fields.

Only one or the other should be specified. These are two ways to represent the "state" of a tool at this workflow step. Both are essentially maps from parameter names to parameter values.

tool_state is much more low-level and expects a flat dictionary with each value a JSON dump. Nested tool structures such as conditionals and repeats should have all their values in the JSON dumped string. In general tool_state may be present in workflows exported from Galaxy but shouldn't be written by humans.

state can contained a typed map. Repeat values can be represented as YAML arrays. An alternative to representing state this way is defining inputs with default values.

Hierarchy

Implemented by

Index

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

This field should not be used in human written Galaxy workflow files.

A typical problem is the referenced tool is not installed, this can be fixed by installed the tool and re-saving the workflow and then re-exporting it.

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

Optional in_

Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.

Optional label

label?: string

A short, human-readable label of this object.

Optional out

out?: (string | WorkflowStepOutput)[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

This can also be called 'outputs' for legacy reasons - but the resulting workflow document is not a valid instance of this schema.

Optional position

position?: StepPosition

Optional run

Specifies a subworkflow to run.

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any

Structured tool state.

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

Optional tool_state

tool_state?: any

Unstructured tool state.

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

Optional type

Workflow step module's type (defaults to 'tool').

Optional uuid

uuid?: string

UUID uniquely representing this element.

Optional when

when?: string

If defined, only run the step when the expression evaluates to true. If false the step is skipped. A skipped step produces a null on each output.

Expression should be an ecma5.1 expression.

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