A documentation string for this object, or an array of strings which should be concatenated.
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.
The unique identifier for this object.
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.
A short, human-readable label of this object.
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.
Specifies a subworkflow to run.
Structured tool state.
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').
The Galaxy Tool Shed repository that should be installed in order to use this tool.
Unstructured tool state.
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.
Workflow step module's type (defaults to 'tool').
UUID uniquely representing this element.
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.
Generated using TypeDoc
Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowStep
This represents a non-input step a Galaxy Workflow.
A note about
state
andtool_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 generaltool_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 representingstate
this way is defining inputs with default values.