Package org.galaxyproject.gxformat2.v19_09

Interface WorkflowStep

All Superinterfaces:
Documented, HasStepErrors, HasStepPosition, HasUUID, Identified, Labeled, ReferencesTool, Savable
All Known Implementing Classes:
WorkflowStepImpl
public interface WorkflowStep extends Identified, Labeled, Documented, HasStepPosition, ReferencesTool, HasStepErrors, HasUUID, Savable
Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowStep
This interface is implemented by WorkflowStepImpl
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.

  • Method Summary

    Modifier and Type
    Method
    Description
    Object
    getDoc()
    Getter for property https://w3id.org/cwl/salad#Documented/doc
    A documentation string for this object, or an array of strings which should be concatenated.
    Optional<String>
    getErrors()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors/errors
    During Galaxy export there may be some problem validating the tool state, tool used, etc..
    Optional<String>
    getId()
    Getter for property https://w3id.org/cwl/cwl#Identified/id
    The unique identifier for this object.
    Optional<List<Object>>
    getIn()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#in
    Defines the input parameters of the workflow step.
    Optional<String>
    getLabel()
    Getter for property https://w3id.org/cwl/cwl#Labeled/label
    A short, human-readable label of this object.
    Optional<List<Object>>
    getOut()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#out
    Defines the parameters representing the output of the process.
    Optional<StepPosition>
    getPosition()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
    Optional<GalaxyWorkflow>
    getRun()
    Getter for property https://w3id.org/cwl/cwl#run
    Specifies a subworkflow to run.
    Optional<List<Object>>
    getRuntime_inputs()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStep/runtime_inputs
    Optional<Object>
    getState()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#state
    Structured tool state.
    Optional<String>
    getTool_id()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
    The tool ID used to run this step of the workflow (e.g.
    Optional<ToolShedRepository>
    getTool_shed_repository()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_shed_repository
    The Galaxy Tool Shed repository that should be installed in order to use this tool.
    Optional<Object>
    getTool_state()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#tool_state
    Unstructured tool state.
    Optional<String>
    getTool_version()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
    The tool version corresponding used to run this step of the workflow.
    Optional<WorkflowStepType>
    getType()
    Getter for property https://w3id.org/cwl/salad#type
    Workflow step module's type (defaults to 'tool').
    Optional<String>
    getUuid()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
    UUID uniquely representing this element.

  • Method Details

    • getId

      Optional<String> getId()
      Getter for property https://w3id.org/cwl/cwl#Identified/id
      The unique identifier for this object. *

    • getLabel

      Optional<String> getLabel()
      Getter for property https://w3id.org/cwl/cwl#Labeled/label
      A short, human-readable label of this object. *
      Specified by:
      getLabel in interface Labeled

    • getDoc

      Object getDoc()
      Getter for property https://w3id.org/cwl/salad#Documented/doc
      A documentation string for this object, or an array of strings which should be concatenated. *
      Specified by:
      getDoc in interface Documented

    • getPosition

      Optional<StepPosition> getPosition()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
      Specified by:
      getPosition in interface HasStepPosition

    • getTool_id

      Optional<String> getTool_id()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
      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'). *
      Specified by:
      getTool_id in interface ReferencesTool

    • getTool_shed_repository

      Optional<ToolShedRepository> getTool_shed_repository()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_shed_repository
      The Galaxy Tool Shed repository that should be installed in order to use this tool. *
      Specified by:
      getTool_shed_repository in interface ReferencesTool

    • getTool_version

      Optional<String> getTool_version()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
      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. *
      Specified by:
      getTool_version in interface ReferencesTool

    • getErrors

      Optional<String> getErrors()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors/errors
      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. *

      Specified by:
      getErrors in interface HasStepErrors

    • getUuid

      Optional<String> getUuid()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
      UUID uniquely representing this element. *
      Specified by:
      getUuid in interface HasUUID

    • getIn

      Optional<List<Object>> getIn()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#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. *

    • getOut

      Optional<List<Object>> getOut()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#out
      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. *

    • getState

      Optional<Object> getState()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#state
      Structured tool state. *

    • getTool_state

      Optional<Object> getTool_state()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#tool_state
      Unstructured tool state. *

    • getType

      Optional<WorkflowStepType> getType()
      Getter for property https://w3id.org/cwl/salad#type
      Workflow step module's type (defaults to 'tool'). *

    • getRun

      Optional<GalaxyWorkflow> getRun()
      Getter for property https://w3id.org/cwl/cwl#run
      Specifies a subworkflow to run. *

    • getRuntime_inputs

      Optional<List<Object>> getRuntime_inputs()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStep/runtime_inputs