CWL parameter mapping

Type mappings

string

Map to Text.

{
    "@id": "#param/in_str",
    "@type": "FormalParameter",
    "additionalType": "Text",
    "name": "in_str"
},
{
    "@id": "#pv/in_str",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_str"},
    "name": "in_str",
    "value": "spam"
}

array

A property in RO-Crate can have a single value or multiple values, so the additionalType can simply be the mapping of the element’s type (e.g., string[] to Text). To register the fact that the workflow allows multiple entries for that parameter, set multipleValues to True:

{
    "@id": "#param/in_array",
    "@type": "FormalParameter",
    "additionalType": "Text",
    "multipleValues": "True",
    "name": "in_array"
},
{
    "@id": "#pv/in_array",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_array"},
    "name": "in_array",
    "value": ["foo", "bar"]
}

This reuses multipleValues from PropertyValueSpecification, similarly to what FormalParameter does for defaultValue and valueRequired.

Any

Map to DataType.

{
    "@id": "#param/in_any",
    "@type": "FormalParameter",
    "additionalType": "DataType",
    "name": "in_any"
},
{
    "@id": "#pv/in_any",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_any"},
    "name": "in_any",
    "value": "tar"
}

boolean

Map to Boolean.

{
    "@id": "#param/in_bool",
    "@type": "FormalParameter",
    "additionalType": "Boolean",
    "name": "in_bool"
},
{
    "@id": "#pv/in_bool",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_bool"},
    "name": "in_bool",
    "value": "True"
}

int, long

Map to Integer.

{
    "@id": "#param/in_int",
    "@type": "FormalParameter",
    "additionalType": "Integer",
    "name": "in_int"
},
{
    "@id": "#pv/in_int",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_int"},
    "name": "in_int",
    "value": "42"
}

float, double

Map to Float.

{
    "@id": "#param/in_float",
    "@type": "FormalParameter",
    "additionalType": "Float",
    "name": "in_float"
},
{
    "@id": "#pv/in_float",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_float"},
    "name": "in_float",
    "value": "3.14"
}

multiple types

Map to array of mappings of each type, e.g., [int, float] to ["Integer", "Float"]. Note that the CWL type array may include "null", indicating that the parameter is optional (and should have a default value): in this case, set valueRequired to False:

{
    "@id": "#param/in_multi",
    "@type": "FormalParameter",
    "additionalType": ["Float", "Integer"],
    "defaultValue": "9.99",
    "name": "in_multi",
    "valueRequired": "False"
},
{
    "@id": "#pv/in_multi",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_multi"},
    "name": "in_multi",
    "value": "9.99"
} 

enum

Map to Text. The set of predefined allowed values can be represented via valuePattern:

{
    "@id": "#param/in_enum",
    "@type": "FormalParameter",
    "additionalType": "Text",
    "name": "in_enum",
    "valuePattern": "A|B"
},
{
    "@id": "#pv/in_enum",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_enum"},
    "name": "in_enum",
    "value": "B"
}

record

Map to PropertyValue. It actually maps to an array of PropertyValues, so multipleValues can be set to True (similarly to the mapping of array). To serialize the actual value of {"in_record_A": "Tom", "in_record_B": "Jerry"}, use nested PropertyValues:

{
    "@id": "#param/in_record",
    "@type": "FormalParameter",
    "additionalType": "PropertyValue",
    "multipleValues": "True",
    "name": "in_record"
},
{
    "@id": "#pv/in_record",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "#param/in_record"},
    "name": "in_record",
    "value": [
        {"@id": "#pv/in_record/in_record_A"},
        {"@id": "#pv/in_record/in_record_B"}
    ]
}
{
    "@id": "#pv/in_record/in_record_A",
    "@type": "PropertyValue",
    "name": "in_record/in_record_A",
    "value": "Tom"
},
{
    "@id": "#pv/in_record/in_record_B",
    "@type": "PropertyValue",
    "name": "in_record/in_record_B",
    "value": "Jerry"
},

In the above example, record keys have been used to set additional slash-separated fields in the @id.

Annotations

format

Use FormalParameter’s encodingFormat:

{
    "@id": "#param/input",
    "@type": "FormalParameter",
    "additionalType": "File",
    "encodingFormat": "https://www.iana.org/assignments/media-types/text/csv",
    "name": "input"
}