cwl

package
v0.9.68 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Jun 6, 2018 License: BSD-2-Clause Imports: 17 Imported by: 6

Documentation

Index

Constants

View Source 
const (
	CWL_Workflow          string = "Workflow"
	CWL_CommandLineTool   string = "CommandLineTool"
	CWL_WorkflowStepInput string = "WorkflowStepInput"
)

CWL Classes (note that type names also are class names)

Variables

View Source 
var ValidClassMap = map[string]string{} // lower-case to correct case mapping
View Source 
var ValidTypeMap = map[CWLType_Type_Basic]CWLType_Type_Basic{} // lower-case to correct case mapping
View Source 
var Valid_Classes = []string{"Workflow", "CommandLineTool", "WorkflowStepInput"}
View Source 
var Valid_Types = []CWLType_Type_Basic{CWL_null, CWL_boolean, CWL_int, CWL_long, CWL_float, CWL_double, CWL_string, CWL_File, CWL_Directory, CWL_Any, CWL_stdin, CWL_stdout, CWL_stderr}

Functions

func AddRequirement added in v0.9.67 

func AddRequirement(new_r Requirement, old_array_ptr *[]Requirement) (new_array_ptr *[]Requirement, err error)

func Add_to_collection_deprecated added in v0.9.67 

func Add_to_collection_deprecated(collection *CWL_collection, object_array CWL_object_array) (err error)

func CreateWorkflowStepInputArray 

func CreateWorkflowStepInputArray(original interface{}) (array_ptr *[]WorkflowStepInput, err error)

func DeleteRequirement added in v0.9.67 

func DeleteRequirement(requirement_class string, old_array_ptr *[]Requirement) (new_array_ptr *[]Requirement, err error)

func GetClass added in v0.9.62 

func GetClass(native interface{}) (class string, err error)

func GetId added in v0.9.62 

func GetId(native interface{}) (id string, err error)

func GetMapElement 

func GetMapElement(m map[interface{}]interface{}, key string) (value interface{}, err error)

func GetSecondaryFilesArray added in v0.9.67 

func GetSecondaryFilesArray(original interface{}) (array []interface{}, err error)

returns array<File | Directory>

func IsValidClass added in v0.9.62 

func IsValidClass(native_str string) (result string, ok bool)

func MakeStringMap added in v0.9.62 

func MakeStringMap(v interface{}) (result interface{}, err error)

func NewBaseCommandArray added in v0.9.48 

func NewBaseCommandArray(original interface{}) (new_array []string, err error)

func NewCWLTypeArray added in v0.9.48 

func NewCWLTypeArray(native interface{}, parent_id string) (cwl_array_ptr *[]CWLType, err error)

func NewCWL_object_array added in v0.9.62 

func NewCWL_object_array(original interface{}) (array CWL_object_array, schemata []CWLType_Type, err error)

func NewCommandLineTool added in v0.9.45 

func NewCommandLineTool(generic interface{}, cwl_version CWLVersion) (commandLineTool *CommandLineTool, schemata []CWLType_Type, err error)

func NewCommandLineTool(object CWL_object_generic) (commandLineTool *CommandLineTool, err error) {

func NewCommandOutputParameterArray added in v0.9.45 

func NewCommandOutputParameterArray(original interface{}, schemata []CWLType_Type) (copa *[]CommandOutputParameter, err error)

func NewCommandOutputParameterType added in v0.9.45 

func NewCommandOutputParameterType(original interface{}, schemata []CWLType_Type) (result interface{}, err error)

func NewCommandOutputParameterTypeArray added in v0.9.45 

func NewCommandOutputParameterTypeArray(original interface{}, schemata []CWLType_Type) (result_array []interface{}, err error)

func NewExpressionArray added in v0.9.62 

func NewExpressionArray(original interface{}) (expressions *[]Expression, err error)

func NewExpressionToolOutputParameterArray added in v0.9.67 

func NewExpressionToolOutputParameterArray(original interface{}, schemata []CWLType_Type) (new_array_ptr *[]ExpressionToolOutputParameter, err error)

func NewNamed_CWL_object_array added in v0.9.67 

func NewNamed_CWL_object_array(original interface{}, cwl_version CWLVersion) (array Named_CWL_object_array, schemata []CWLType_Type, err error)

func NewNamed_CWL_object_from_interface added in v0.9.67 

func NewNamed_CWL_object_from_interface(original interface{}, cwl_version CWLVersion) (x Named_CWL_object, schemata []CWLType_Type, err error)

func NewRequirement 

func NewRequirement(class string, obj interface{}) (r Requirement, schemata []CWLType_Type, err error)

func NewSchemaDefRequirement added in v0.9.67 

func NewSchemaDefRequirement(original interface{}) (r *SchemaDefRequirement, schemata []CWLType_Type, err error)

func NewWorkflow added in v0.9.45 

func NewWorkflow(original interface{}, cwl_version CWLVersion) (workflow_ptr *Workflow, schemata []CWLType_Type, err error)

func NewWorkflowOutputParameterArray added in v0.9.45 

func NewWorkflowOutputParameterArray(original interface{}, schemata []CWLType_Type) (new_array_ptr *[]WorkflowOutputParameter, err error)

WorkflowOutputParameter

func NewWorkflowOutputParameterType added in v0.9.45 

func NewWorkflowOutputParameterType(original interface{}, schemata []CWLType_Type) (result interface{}, err error)

func NewWorkflowOutputParameterTypeArray added in v0.9.45 

func NewWorkflowOutputParameterTypeArray(original interface{}, schemata []CWLType_Type) (result interface{}, err error)

func NewWorkflowStep added in v0.9.45 

func NewWorkflowStep(original interface{}, CwlVersion CWLVersion) (w *WorkflowStep, schemata []CWLType_Type, err error)

func New_CWL_object added in v0.9.62 

func New_CWL_object(original interface{}, cwl_version CWLVersion) (obj CWL_object, schemata []CWLType_Type, err error)

func NormalizeOutputParameter added in v0.9.67 

func NormalizeOutputParameter(original_map map[string]interface{}) (err error)

func Parse_cwl_document 

func Parse_cwl_document(yaml_str string) (object_array Named_CWL_object_array, cwl_version CWLVersion, schemata []CWLType_Type, err error)

func TypeIsCorrect added in v0.9.62 

func TypeIsCorrect(allowed_types []CWLType_Type, object CWLType) (ok bool, err error)

func TypeIsCorrectSingle added in v0.9.62 

func TypeIsCorrectSingle(schema CWLType_Type, object CWLType) (ok bool, err error)

func Unmarshal 

func Unmarshal(data_ptr *[]byte, v interface{}) (err error)

Types

type Any 

type Any interface {
	CWL_class
}

func NewAny added in v0.9.45 

func NewAny(native interface{}) (any Any, err error)

type Array added in v0.9.62 

type Array []CWLType

func NewArray added in v0.9.62 

func NewArray(id string, native interface{}) (array_ptr *Array, err error)

func (*Array) GetClass added in v0.9.62 

func (c *Array) GetClass() string

func (*Array) GetId added in v0.9.62 

func (c *Array) GetId() string

func (*Array) GetType added in v0.9.62 

func (c *Array) GetType() CWLType_Type

func (*Array) Is_CWL_minimal added in v0.9.62 

func (c *Array) Is_CWL_minimal()

func (*Array) Is_CWL_object added in v0.9.67 

func (c *Array) Is_CWL_object()

func (*Array) SetId added in v0.9.62 

func (c *Array) SetId(string)

func (*Array) String added in v0.9.62 

func (c *Array) String() string

func NewArray(id string, native interface{}) (array *Array, err error) { 

	//array = &Array{CWLType_Impl: CWLType_Impl{Id: id}}
	//array = &Array{}
	//array.Class = "array"
	//schema := NewArraySchema()
	//array.Type = CWL_array
	//array.Type =

	//if id != "" {
	//		array.Id = id
	//	}

	switch native.(type) {
	case map[string]interface{}:
		native_map := native.(map[string]interface{})

		obj_id, has_id := native_map["id"]
		if has_id {
			obj_id_str, ok := obj_id.(string)
			if !ok {
				err = fmt.Errorf("(NewArray) id is not of type string")
				return
			}

			array.Id = obj_id_str
		}

		items, has_items := native_map["items"]
		if has_items {
			var item_array *[]CWLType
			item_array, err = NewCWLTypeArray(items, array.Id)
			if err != nil {
				err = fmt.Errorf("(NewArray) NewCWLTypeArray failed: %s", err.Error())
				return
			}

			array.Items = *item_array

			//type_map := make(map[CWLType_Type]bool)

			// collect info about types used in the array, needed later for verification
			//for _, item := range array.Items {

			//	item_type := item.GetType()
			//	type_map[item_type] = true

			//}

			//for item_type, _ := range type_map {
			//	schema.Items = append(schema.Items, item_type)
			//}

			//a_type := array.Items[0]
			//array.Items_Type = a_type.GetType()
		}

	case []interface{}:
		native_array := native.([]interface{})
		for _, value := range native_array {

			value_cwl, xerr := NewCWLType("", value)
			if xerr != nil {
				err = xerr
				return
			}

			array.Items = append(array.Items, value_cwl)
		}
		//if len(array.Items) > 0 {
		//	array.Items_Type = array.Items[0].GetType()
		//}
		return
	default:
		err = fmt.Errorf("(NewArray) type %s unknown", reflect.TypeOf(native))
		return
	}

	return
}

type ArraySchema added in v0.9.62 

type ArraySchema struct {
	Items []CWLType_Type `yaml:"items,omitempty" bson:"items,omitempty" json:"items,omitempty" mapstructure:"items,omitempty"` // string or []string ([] speficies which types are possible, e.g ["File" , "null"])
	Type  string         `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty" mapstructure:"type,omitempty"`     // must be array
	Label string         `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
}

func NewArraySchema added in v0.9.62 

func NewArraySchema() *ArraySchema

func (*ArraySchema) GetId added in v0.9.67 

func (c *ArraySchema) GetId() string

func (*ArraySchema) Is_Type added in v0.9.62 

func (c *ArraySchema) Is_Type()

func (*ArraySchema) Type2String added in v0.9.62 

func (c *ArraySchema) Type2String() string

type BaseRequirement added in v0.9.62 

type BaseRequirement struct {
	Class string `yaml:"class,omitempty" json:"class,omitempty" bson:"class,omitempty" mapstructure:"class,omitempty"`
}

func (BaseRequirement) GetClass added in v0.9.62 

func (c BaseRequirement) GetClass() string

type Boolean added in v0.9.45 

type Boolean bool

func NewBoolean added in v0.9.62 

func NewBoolean(id string, value bool) (b *Boolean)

func NewBooleanFromInterface added in v0.9.62 

func NewBooleanFromInterface(id string, native interface{}) (b *Boolean, err error)

func NewBooleanFrombool added in v0.9.62 

func NewBooleanFrombool(value bool) (b *Boolean)

func (*Boolean) GetClass added in v0.9.45 

func (b *Boolean) GetClass() string

func (*Boolean) GetId added in v0.9.45 

func (b *Boolean) GetId() string

func (*Boolean) GetType added in v0.9.62 

func (b *Boolean) GetType() CWLType_Type

func (*Boolean) Is_CWL_minimal added in v0.9.62 

func (b *Boolean) Is_CWL_minimal()

func (*Boolean) Is_CWL_object added in v0.9.67 

func (b *Boolean) Is_CWL_object()

func (*Boolean) SetId added in v0.9.45 

func (b *Boolean) SetId(i string)

func (*Boolean) String added in v0.9.45 

func (b *Boolean) String() string

type CWLType 

type CWLType interface {
	CWL_object
	CWL_class // is an interface
	//Is_CommandInputParameterType()
	//Is_CommandOutputParameterType()
	GetType() CWLType_Type
	String() string
}

CWLType - CWL basic types: int, string, boolean, .. etc http://www.commonwl.org/v1.0/CommandLineTool.html#CWLType null, boolean, int, long, float, double, string, File, Directory

func NewCWLType added in v0.9.45 

func NewCWLType(id string, native interface{}) (cwl_type CWLType, err error)

func NewCWLTypeByClass added in v0.9.62 

func NewCWLTypeByClass(class string, id string, native interface{}) (cwl_type CWLType, err error)

type CWLType_Impl added in v0.9.45 

type CWLType_Impl struct {
	CWL_object_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"`
	CWL_class_Impl  `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // Provides: Id, Class
	Type            CWLType_Type                                                          `yaml:"-" json:"-" bson:"-" mapstructure:"-"`
}

func (*CWLType_Impl) GetType added in v0.9.62 

func (c *CWLType_Impl) GetType() CWLType_Type

func (*CWLType_Impl) Is_CWLType added in v0.9.62 

func (c *CWLType_Impl) Is_CWLType()

func (*CWLType_Impl) Is_CWL_minimal added in v0.9.62 

func (c *CWLType_Impl) Is_CWL_minimal()

type CWLType_Type added in v0.9.62 

type CWLType_Type interface {
	Is_Type()
	Type2String() string
	GetId() string
}

func CreateRequirementArray 

func CreateRequirementArray(original interface{}) (new_array_ptr *[]Requirement, schemata []CWLType_Type, err error)

func CreateWorkflowStepsArray 

func CreateWorkflowStepsArray(original interface{}, CwlVersion CWLVersion) (schemata []CWLType_Type, array_ptr *[]WorkflowStep, err error)

CreateWorkflowStepsArray

func GetProcess added in v0.9.67 

func GetProcess(original interface{}, collection *CWL_collection, CwlVersion CWLVersion, input_schemata []CWLType_Type) (process interface{}, schemata []CWLType_Type, err error)

func NewCWLType_Type added in v0.9.62 

func NewCWLType_Type(schemata []CWLType_Type, native interface{}, context string) (result CWLType_Type, err error)

func NewCWLType_TypeArray added in v0.9.62 

func NewCWLType_TypeArray(native interface{}, schemata []CWLType_Type, context string, pass_schemata_along bool) (result []CWLType_Type, err error)

func NewCWLType_TypeFromString added in v0.9.62 

func NewCWLType_TypeFromString(schemata []CWLType_Type, native string, context string) (result CWLType_Type, err error)

func NewCommandInputParameterTypeArray added in v0.9.62 

func NewCommandInputParameterTypeArray(original interface{}, schemata []CWLType_Type) (result []CWLType_Type, err error)

func NewProcess added in v0.9.45 

func NewProcess(original interface{}, CwlVersion CWLVersion) (process interface{}, schemata []CWLType_Type, err error)

returns CommandLineTool, ExpressionTool or Workflow

type CWLType_Type_Basic added in v0.9.62 

type CWLType_Type_Basic string
const (
	CWL_null      CWLType_Type_Basic = "null"      //no value
	CWL_boolean   CWLType_Type_Basic = "boolean"   //a binary value
	CWL_int       CWLType_Type_Basic = "int"       //32-bit signed integer
	CWL_long      CWLType_Type_Basic = "long"      //64-bit signed integer
	CWL_float     CWLType_Type_Basic = "float"     //single precision (32-bit) IEEE 754 floating-point number
	CWL_double    CWLType_Type_Basic = "double"    //double precision (64-bit) IEEE 754 floating-point number
	CWL_string    CWLType_Type_Basic = "string"    //Unicode character sequence
	CWL_File      CWLType_Type_Basic = "File"      //A File object
	CWL_Directory CWLType_Type_Basic = "Directory" //A Directory object
	CWL_Any       CWLType_Type_Basic = "Any"       //A Any object

	CWL_stdin  CWLType_Type_Basic = "stdin"
	CWL_stdout CWLType_Type_Basic = "stdout"
	CWL_stderr CWLType_Type_Basic = "stderr"

	CWL_array   CWLType_Type_Basic = "array"   // unspecific type, only useful as a struct with items
	CWL_record  CWLType_Type_Basic = "record"  // unspecific type
	CWL_enum    CWLType_Type_Basic = "enum"    // unspecific type
	CWL_pointer CWLType_Type_Basic = "pointer" // unspecific type
)

CWL Types http://www.commonwl.org/draft-3/CommandLineTool.html#CWLType

func IsValidType added in v0.9.62 

func IsValidType(native_str string) (result CWLType_Type_Basic, ok bool)

func (CWLType_Type_Basic) GetId added in v0.9.67 

func (s CWLType_Type_Basic) GetId() string

func (CWLType_Type_Basic) Is_Type added in v0.9.62 

func (s CWLType_Type_Basic) Is_Type()

func (CWLType_Type_Basic) Type2String added in v0.9.62 

func (s CWLType_Type_Basic) Type2String() string

type CWLVersion 

type CWLVersion string

type CWL_array_type added in v0.9.62 

type CWL_array_type interface {
	Is_CWL_array_type()
	Get_Array() *[]CWLType
}

type CWL_class added in v0.9.67 

type CWL_class interface {
	//CWL_minimal_interface
	GetClass() string
}

type CWL_class_Impl added in v0.9.67 

type CWL_class_Impl struct {
	//Id    string `yaml:"id,omitempty" json:"id,omitempty" bson:"id,omitempty"`
	Class string `yaml:"class,omitempty" json:"class,omitempty" bson:"class,omitempty"`
}

func (*CWL_class_Impl) GetClass added in v0.9.67 

func (c *CWL_class_Impl) GetClass() string

type CWL_collection 

type CWL_collection struct {
	Workflows          map[string]*Workflow
	WorkflowStepInputs map[string]*WorkflowStepInput
	CommandLineTools   map[string]*CommandLineTool
	ExpressionTools    map[string]*ExpressionTool

	Files    map[string]*File
	Strings  map[string]*String
	Ints     map[string]*Int
	Booleans map[string]*Boolean
	All      map[string]CWL_object // everything goes in here
	//Job_input          *Job_document
	Job_input_map *JobDocMap

	Schemata map[string]CWLType_Type
}

func NewCWL_collection 

func NewCWL_collection() (collection CWL_collection)

func (CWL_collection) Add 

func (c CWL_collection) Add(id string, obj CWL_object) (err error)

func (CWL_collection) AddArray added in v0.9.67 

func (c CWL_collection) AddArray(object_array Named_CWL_object_array) (err error)

func (CWL_collection) AddSchemata added in v0.9.67 

func (c CWL_collection) AddSchemata(obj []CWLType_Type) (err error)

func (CWL_collection) Evaluate 

func (c CWL_collection) Evaluate(raw string) (parsed string)

func (CWL_collection) Get 

func (c CWL_collection) Get(id string) (obj CWL_object, err error)

func (CWL_collection) GetCWLType added in v0.9.62 

func (c CWL_collection) GetCWLType(id string) (obj CWLType, err error)

func (CWL_collection) GetCommandLineTool added in v0.9.62 

func (c CWL_collection) GetCommandLineTool(id string) (obj *CommandLineTool, err error)

func (CWL_collection) GetExpressionTool added in v0.9.67 

func (c CWL_collection) GetExpressionTool(id string) (obj *ExpressionTool, err error)

func (CWL_collection) GetFile 

func (c CWL_collection) GetFile(id string) (obj *File, err error)

func (CWL_collection) GetInt 

func (c CWL_collection) GetInt(id string) (obj *Int, err error)

func (CWL_collection) GetSchemata added in v0.9.67 

func (c CWL_collection) GetSchemata() (obj []CWLType_Type, err error)

func (CWL_collection) GetString 

func (c CWL_collection) GetString(id string) (obj *String, err error)

func (CWL_collection) GetWorkflow added in v0.9.62 

func (c CWL_collection) GetWorkflow(id string) (obj *Workflow, err error)

func (CWL_collection) GetWorkflowStepInput 

func (c CWL_collection) GetWorkflowStepInput(id string) (obj *WorkflowStepInput, err error)

type CWL_document_generic 

type CWL_document_generic struct {
	CwlVersion CWLVersion    `yaml:"cwlVersion"`
	Graph      []interface{} `yaml:"graph"`
}

this is used by YAML or JSON library for inital parsing

type CWL_id added in v0.9.67 

type CWL_id interface {
	//CWL_bbject_interface
	//GetClass() string
	GetId() string
	SetId(string)
}

type CWL_id_Impl added in v0.9.67 

type CWL_id_Impl struct {
	Id string `yaml:"id,omitempty" json:"id,omitempty" bson:"id,omitempty"`
}

func (*CWL_id_Impl) GetId added in v0.9.67 

func (c *CWL_id_Impl) GetId() string

func (*CWL_id_Impl) SetId added in v0.9.67 

func (c *CWL_id_Impl) SetId(id string)

type CWL_object 

type CWL_object interface {
	Is_CWL_object()
}

func CreateListingArray added in v0.9.67 

func CreateListingArray(original interface{}) (array []CWL_object, err error)

func NewListingFromInterface added in v0.9.67 

func NewListingFromInterface(original interface{}) (obj CWL_object, err error)

type CWL_object_Impl added in v0.9.62 

type CWL_object_Impl struct{}

func (*CWL_object_Impl) Is_CWL_object added in v0.9.67 

func (c *CWL_object_Impl) Is_CWL_object()

type CWL_object_array added in v0.9.62 

type CWL_object_array []CWL_object

type CWL_object_generic 

type CWL_object_generic map[string]interface{}

type CommandInputArraySchema added in v0.9.67 

type CommandInputArraySchema struct {
	ArraySchema  `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	InputBinding *CommandLineBinding `yaml:"inputBinding,omitempty" bson:"inputBinding,omitempty" json:"inputBinding,omitempty"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputArraySchema

func NewCommandInputArraySchema added in v0.9.67 

func NewCommandInputArraySchema() (coas *CommandInputArraySchema)

func NewCommandInputArraySchemaFromInterface added in v0.9.67 

func NewCommandInputArraySchemaFromInterface(original interface{}, schemata []CWLType_Type) (coas *CommandInputArraySchema, err error)

func (*CommandInputArraySchema) GetId added in v0.9.67 

func (c *CommandInputArraySchema) GetId() string

func (*CommandInputArraySchema) Type2String added in v0.9.67 

func (c *CommandInputArraySchema) Type2String() string

type CommandInputParameter 

type CommandInputParameter struct {
	Id             string   `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty" mapstructure:"id,omitempty"`
	SecondaryFiles []string `` // TODO string | Expression | array<string | Expression>
	/* 135-byte string literal not displayed */
	Format       []string           `yaml:"format,omitempty" bson:"format,omitempty" json:"format,omitempty" mapstructure:"format,omitempty"`
	Streamable   bool               `yaml:"streamable,omitempty" bson:"streamable,omitempty" json:"streamable,omitempty" mapstructure:"streamable,omitempty"`
	Type         []CWLType_Type     `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty" mapstructure:"type,omitempty"` // []CommandInputParameterType  CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string | array<CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string>
	Label        string             `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
	Description  string             `yaml:"description,omitempty" bson:"description,omitempty" json:"description,omitempty" mapstructure:"description,omitempty"`
	InputBinding CommandLineBinding `yaml:"inputBinding" bson:"inputBinding" json:"inputBinding" mapstructure:"inputBinding"`
	Default      CWLType            `yaml:"default,omitempty" bson:"default,omitempty" json:"default,omitempty" mapstructure:"default,omitempty"`
}

func CreateCommandInputArray 

func CreateCommandInputArray(original interface{}, schemata []CWLType_Type) (err error, new_array []*CommandInputParameter)

keyname will be converted into 'Id'-field array<CommandInputParameter> | map<CommandInputParameter.id, CommandInputParameter.type> | map<CommandInputParameter.id, CommandInputParameter>

func NewCommandInputParameter added in v0.9.45 

func NewCommandInputParameter(v interface{}, schemata []CWLType_Type) (input_parameter *CommandInputParameter, err error)

type CommandInputRecordField added in v0.9.67 

type CommandInputRecordField struct {
	RecordField `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#InputRecordField

func CreateCommandInputRecordFieldArray added in v0.9.67 

func CreateCommandInputRecordFieldArray(native []interface{}, schemata []CWLType_Type) (irfa []CommandInputRecordField, err error)

func NewCommandInputRecordField added in v0.9.67 

func NewCommandInputRecordField(native interface{}, schemata []CWLType_Type) (crf *CommandInputRecordField, err error)

type CommandInputRecordSchema added in v0.9.67 

type CommandInputRecordSchema struct {
	RecordSchema `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // provides Type, Label, Name
	Fields       []CommandInputRecordField                                             `yaml:"fields,omitempty" json:"fields,omitempty" bson:"fields,omitempty"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputRecordSchema

func NewCommandInputRecordSchema added in v0.9.67 

func NewCommandInputRecordSchema(native_map map[string]interface{}) (cirs *CommandInputRecordSchema, err error)

func NewCommandInputRecordSchemaFromInterface added in v0.9.67 

func NewCommandInputRecordSchemaFromInterface(native interface{}, schemata []CWLType_Type) (cirs *CommandInputRecordSchema, err error)

type CommandLineBinding 

type CommandLineBinding struct {
	LoadContents  bool        `` /* 127-byte string literal not displayed */
	Position      int         `yaml:"position,omitempty" bson:"position,omitempty" json:"position,omitempty" mapstructure:"position,omitempty"`
	Prefix        string      `yaml:"prefix,omitempty" bson:"prefix,omitempty" json:"prefix,omitempty" mapstructure:"prefix,omitempty"`
	Separate      bool        `yaml:"separate,omitempty" bson:"separate,omitempty" json:"separate,omitempty" mapstructure:"separate,omitempty"`
	ItemSeparator string      `` /* 131-byte string literal not displayed */
	ValueFrom     *Expression `yaml:"valueFrom,omitempty" bson:"valueFrom,omitempty" json:"valueFrom,omitempty" mapstructure:"valueFrom,omitempty"`
	ShellQuote    bool        `yaml:"shellQuote,omitempty" bson:"shellQuote,omitempty" json:"shellQuote,omitempty" mapstructure:"shellQuote,omitempty"`
}

http://www.commonwl.org/v1.0/Workflow.html#CommandLineBinding

func NewCommandLineBinding added in v0.9.48 

func NewCommandLineBinding(original interface{}) (clb *CommandLineBinding, err error)

func NewCommandLineBindingArray added in v0.9.48 

func NewCommandLineBindingArray(original interface{}) (new_array []CommandLineBinding, err error)

type CommandLineTool 

type CommandLineTool struct {
	//Id                 string                   `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty"`
	//Class              string                   `yaml:"class,omitempty" bson:"class,omitempty" json:"class,omitempty"`
	CWL_object_Impl    `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	CWL_class_Impl     `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	CWL_id_Impl        `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	BaseCommand        []string                 `yaml:"baseCommand,omitempty" bson:"baseCommand,omitempty" json:"baseCommand,omitempty" mapstructure:"baseCommand,omitempty"`
	Inputs             []CommandInputParameter  `yaml:"inputs" bson:"inputs" json:"inputs" mapstructure:"inputs"`
	Outputs            []CommandOutputParameter `yaml:"outputs" bson:"outputs" json:"outputs" mapstructure:"outputs"`
	Hints              []Requirement            `yaml:"hints,omitempty" bson:"hints,omitempty" json:"hints,omitempty" mapstructure:"hints,omitempty"`
	Requirements       *[]Requirement           `` /* 127-byte string literal not displayed */
	Doc                string                   `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty" mapstructure:"doc,omitempty"`
	Label              string                   `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
	Description        string                   `yaml:"description,omitempty" bson:"description,omitempty" json:"description,omitempty" mapstructure:"description,omitempty"`
	CwlVersion         CWLVersion               `yaml:"cwlVersion,omitempty" bson:"cwlVersion,omitempty" json:"cwlVersion,omitempty" mapstructure:"cwlVersion,omitempty"`
	Arguments          []CommandLineBinding     `yaml:"arguments,omitempty" bson:"arguments,omitempty" json:"arguments,omitempty" mapstructure:"arguments,omitempty"`
	Stdin              string                   `yaml:"stdin,omitempty" bson:"stdin,omitempty" json:"stdin,omitempty" mapstructure:"stdin,omitempty"`     // TODO support Expression
	Stderr             string                   `yaml:"stderr,omitempty" bson:"stderr,omitempty" json:"stderr,omitempty" mapstructure:"stderr,omitempty"` // TODO support Expression
	Stdout             string                   `yaml:"stdout,omitempty" bson:"stdout,omitempty" json:"stdout,omitempty" mapstructure:"stdout,omitempty"` // TODO support Expression
	SuccessCodes       []int                    ``                                                                                                        /* 127-byte string literal not displayed */
	TemporaryFailCodes []int                    ``                                                                                                        /* 151-byte string literal not displayed */
	PermanentFailCodes []int                    ``                                                                                                        /* 151-byte string literal not displayed */
}

http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool

func (*CommandLineTool) Is_CWL_minimal added in v0.9.62 

func (c *CommandLineTool) Is_CWL_minimal()

func (*CommandLineTool) Is_process added in v0.9.62 

func (c *CommandLineTool) Is_process()

type CommandOutputArraySchema added in v0.9.45 

type CommandOutputArraySchema struct {
	ArraySchema   `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	OutputBinding *CommandOutputBinding `` /* 131-byte string literal not displayed */
}

func NewCommandOutputArraySchema added in v0.9.45 

func NewCommandOutputArraySchema() (coas *CommandOutputArraySchema)

func NewCommandOutputArraySchemaFromInterface added in v0.9.62 

func NewCommandOutputArraySchemaFromInterface(original interface{}, schemata []CWLType_Type) (coas *CommandOutputArraySchema, err error)

func (*CommandOutputArraySchema) GetId added in v0.9.67 

func (c *CommandOutputArraySchema) GetId() string

func (*CommandOutputArraySchema) Type2String added in v0.9.62 

func (c *CommandOutputArraySchema) Type2String() string

type CommandOutputBinding 

type CommandOutputBinding struct {
	Glob         *[]Expression `yaml:"glob,omitempty" bson:"glob,omitempty" json:"glob,omitempty"`
	LoadContents bool          `` /* 128-byte string literal not displayed */
	OutputEval   *Expression   `yaml:"outputEval,omitempty" bson:"outputEval,omitempty" json:"outputEval,omitempty" mapstructure:"outputEval,omitempty"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding

func NewCommandOutputBinding added in v0.9.45 

func NewCommandOutputBinding(original interface{}) (commandOutputBinding *CommandOutputBinding, err error)

type CommandOutputEnumSchema added in v0.9.45 

type CommandOutputEnumSchema struct {
	EnumSchema    `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // provides Symbols, Type, Label
	OutputBinding *CommandOutputBinding                                                 `` /* 131-byte string literal not displayed */
}

http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputEnumSchema

func NewCommandOutputEnumSchema added in v0.9.62 

func NewCommandOutputEnumSchema(v map[string]interface{}) (schema *CommandOutputEnumSchema, err error)

func (*CommandOutputEnumSchema) GetId added in v0.9.67 

func (c *CommandOutputEnumSchema) GetId() string

func (*CommandOutputEnumSchema) Is_Type added in v0.9.62 

func (c *CommandOutputEnumSchema) Is_Type()

func (c *CommandOutputEnumSchema) Is_CommandOutputParameterType() {}

func (*CommandOutputEnumSchema) Type2String added in v0.9.62 

func (c *CommandOutputEnumSchema) Type2String() string

type CommandOutputParameter 

type CommandOutputParameter struct {
	OutputParameter `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	//Id             string                `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty"`
	//SecondaryFiles []Expression          `yaml:"secondaryFiles,omitempty" bson:"secondaryFiles,omitempty" json:"secondaryFiles,omitempty"` // TODO string | Expression | array<string | Expression>
	//Format         Expression            `yaml:"format,omitempty" bson:"format,omitempty" json:"format,omitempty"`
	//Streamable bool          `yaml:"streamable,omitempty" bson:"streamable,omitempty" json:"streamable,omitempty"`
	//Type []interface{} `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty"` // []CommandOutputParameterType TODO CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string | array<CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string>
	//Label          string                `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty"`
	Description string `yaml:"description,omitempty" bson:"description,omitempty" json:"description,omitempty" mapstructure:"description,omitempty"`
}

func NewCommandOutputParameter added in v0.9.45 

func NewCommandOutputParameter(original interface{}, schemata []CWLType_Type) (output_parameter *CommandOutputParameter, err error)

type CommandOutputRecordField added in v0.9.45 

type CommandOutputRecordField struct{}

type CommandOutputRecordSchema added in v0.9.45 

type CommandOutputRecordSchema struct {
	Type   string                     `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty" mapstructure:"type,omitempty"` // Must be record
	Fields []CommandOutputRecordField `yaml:"fields,omitempty" bson:"fields,omitempty" json:"fields,omitempty" mapstructure:"fields,omitempty"`
	Label  string                     `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
}

func NewCommandOutputRecordSchema added in v0.9.62 

func NewCommandOutputRecordSchema(v interface{}) (schema *CommandOutputRecordSchema, err error)

func (*CommandOutputRecordSchema) GetId added in v0.9.67 

func (c *CommandOutputRecordSchema) GetId() string

func (*CommandOutputRecordSchema) Is_Type added in v0.9.62 

func (c *CommandOutputRecordSchema) Is_Type()

func (c *CommandOutputRecordSchema) Is_CommandOutputParameterType() {}

func (*CommandOutputRecordSchema) Type2String added in v0.9.62 

func (c *CommandOutputRecordSchema) Type2String() string

type Directory 

type Directory struct {
	CWLType_Impl `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // Provides: Id, Class, Type

	Location string        `yaml:"location,omitempty" json:"location,omitempty" bson:"location,omitempty" mapstructure:"location,omitempty"` //
	Path     string        `yaml:"path,omitempty" json:"path,omitempty" bson:"path,omitempty" mapstructure:"path,omitempty"`
	Basename string        `yaml:"basename,omitempty" json:"basename,omitempty" bson:"basename,omitempty" mapstructure:"basename,omitempty"`
	Listing  []interface{} `yaml:"listing,omitempty" json:"listing,omitempty" bson:"listing,omitempty" mapstructure:"listing,omitempty"`
}

func NewDirectory added in v0.9.62 

func NewDirectory() (d *Directory)

func NewDirectoryFromInterface added in v0.9.62 

func NewDirectoryFromInterface(obj interface{}) (d *Directory, err error)

func (Directory) GetClass 

func (d Directory) GetClass() string

func (Directory) String 

func (d Directory) String() string

type Dirent added in v0.9.67 

type Dirent struct {
	CWLType_Impl `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	Entry        Expression `yaml:"entry" json:"entry" bson:"entry" mapstructure:"entry"`
	Entryname    Expression `yaml:"entryname" json:"entryname" bson:"entryname" mapstructure:"entryname"`
	Writable     bool       `yaml:"writable" json:"writable" bson:"writable" mapstructure:"writable"`
}

Dirent http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent

func NewDirentFromInterface added in v0.9.67 

func NewDirentFromInterface(id string, original interface{}) (dirent *Dirent, err error)

type DockerRequirement 

type DockerRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
	DockerPull      string `yaml:"dockerPull,omitempty" bson:"dockerPull,omitempty" json:"dockerPull,omitempty"`
	DockerLoad      string `yaml:"dockerLoad,omitempty" bson:"dockerLoad,omitempty" json:"dockerLoad,omitempty"`
	DockerFile      string `yaml:"dockerFile,omitempty" bson:"dockerFile,omitempty" json:"dockerFile,omitempty"`
	DockerImport    string `yaml:"dockerImport,omitempty" bson:"dockerImport,omitempty" json:"dockerImport,omitempty"`
	DockerImageId   string `yaml:"dockerImageId,omitempty" bson:"dockerImageId,omitempty" json:"dockerImageId,omitempty"`
}

func NewDockerRequirement added in v0.9.62 

func NewDockerRequirement(original interface{}) (r *DockerRequirement, err error)

func (DockerRequirement) GetId 

func (c DockerRequirement) GetId() string

type Double added in v0.9.62 

type Double float64

func NewDouble added in v0.9.62 

func NewDouble(value float64) *Double

func NewDoubleFromInterface added in v0.9.62 

func NewDoubleFromInterface(native interface{}) (i *Double, err error)

func NewDoubleFromfloat64 added in v0.9.62 

func NewDoubleFromfloat64(value float64) (i *Double)

func (*Double) GetClass added in v0.9.62 

func (i *Double) GetClass() string

func (*Double) GetId added in v0.9.62 

func (i *Double) GetId() string

func (*Double) GetType added in v0.9.62 

func (i *Double) GetType() CWLType_Type

func (*Double) Is_CWL_minimal added in v0.9.62 

func (i *Double) Is_CWL_minimal()

func (*Double) Is_CWL_object added in v0.9.67 

func (i *Double) Is_CWL_object()

func (*Double) SetId added in v0.9.62 

func (i *Double) SetId(x string)

func (*Double) String added in v0.9.62 

func (i *Double) String() string

type DummyRequirement added in v0.9.62 

type DummyRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
}

type Empty 

type Empty struct {
	CWLType_Impl `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	Id           string `yaml:"id,omitempty" json:"id,omitempty" bson:"id,omitempty"`
	Class        string `yaml:"class,omitempty" json:"class,omitempty" bson:"class,omitempty"`
}

this is a generic CWL_object. Its only purpose is to retrieve the value of "class"

func NewEmpty added in v0.9.45 

func NewEmpty(value interface{}) (obj_empty *Empty, err error)

func (Empty) GetClass 

func (e Empty) GetClass() string

func (Empty) GetId 

func (e Empty) GetId() string

func (Empty) String 

func (e Empty) String() string

type Enum added in v0.9.62 

type Enum string

func NewEnum added in v0.9.67 

func NewEnum(id string, value string) (s *Enum)

func NewEnumFromInterface added in v0.9.67 

func NewEnumFromInterface(id string, native interface{}) (s *Enum, err error)

func NewEnumFromstring added in v0.9.67 

func NewEnumFromstring(value string) (s *Enum)

func (*Enum) GetClass added in v0.9.62 

func (s *Enum) GetClass() string

func (*Enum) GetId added in v0.9.67 

func (s *Enum) GetId() string

func (*Enum) GetType added in v0.9.67 

func (s *Enum) GetType() CWLType_Type

func (*Enum) Is_CWL_minimal added in v0.9.67 

func (s *Enum) Is_CWL_minimal()

func (*Enum) Is_CWL_object added in v0.9.67 

func (s *Enum) Is_CWL_object()

func (*Enum) SetId added in v0.9.67 

func (s *Enum) SetId(i string)

func (*Enum) String added in v0.9.67 

func (s *Enum) String() string

type EnumSchema added in v0.9.67 

type EnumSchema struct {
	Symbols []string `yaml:"symbols,omitempty" bson:"symbols,omitempty" json:"symbols,omitempty" mapstructure:"symbols,omitempty"`
	Type    string   `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty" mapstructure:"type,omitempty"` // must be enum
	Label   string   `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
	Name    string   `yaml:"name,omitempty" bson:"name,omitempty" json:"name,omitempty" mapstructure:"name,omitempty"`
}

func NewEnumSchemaFromInterface added in v0.9.67 

func NewEnumSchemaFromInterface(original interface{}) (es EnumSchema, err error)

func (EnumSchema) GetId added in v0.9.67 

func (s EnumSchema) GetId() string

func (EnumSchema) Is_Type added in v0.9.67 

func (s EnumSchema) Is_Type()

func (EnumSchema) Type2String added in v0.9.67 

func (s EnumSchema) Type2String() string

type EnvVarRequirement added in v0.9.62 

type EnvVarRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
	EnvDef          []EnvironmentDef `yaml:"envDef,omitempty" bson:"envDef,omitempty" json:"envDef,omitempty" mapstructure:"envDef,omitempty"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#EnvVarRequirement

func NewEnvVarRequirement added in v0.9.62 

func NewEnvVarRequirement(original interface{}) (r *EnvVarRequirement, err error)

func (EnvVarRequirement) GetId added in v0.9.62 

func (c EnvVarRequirement) GetId() string

type EnvironmentDef added in v0.9.62 

type EnvironmentDef struct {
	EnvName  string     `yaml:"envName,omitempty" bson:"envName,omitempty" json:"envName,omitempty" mapstructure:"envName,omitempty"`
	EnvValue Expression `yaml:"envValue,omitempty" bson:"envValue,omitempty" json:"envValue,omitempty" mapstructure:"envValue,omitempty"`
}

func GetEnfDefArray added in v0.9.67 

func GetEnfDefArray(original interface{}) (array []EnvironmentDef, err error)

func NewEnvironmentDefFromInterface added in v0.9.67 

func NewEnvironmentDefFromInterface(original interface{}) (enfDev EnvironmentDef, err error)

type Expression 

type Expression string

func NewExpression added in v0.9.62 

func NewExpression(original interface{}) (expression *Expression, err error)

func NewExpressionFromString added in v0.9.67 

func NewExpressionFromString(original string) (expression *Expression, err error)

var CWL_Expression CWLType_Type = "expression"

func (Expression) String 

func (e Expression) String() string

type ExpressionTool added in v0.9.67 

type ExpressionTool struct {
	CWL_object_Impl `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	CWL_class_Impl  `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	CWL_id_Impl     `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	Inputs          []InputParameter                `yaml:"inputs" bson:"inputs" json:"inputs" mapstructure:"inputs"`
	Outputs         []ExpressionToolOutputParameter `yaml:"outputs" bson:"outputs" json:"outputs" mapstructure:"outputs"`
	Expression      Expression                      `yaml:"expression,omitempty" bson:"expression,omitempty" json:"expression,omitempty" mapstructure:"expression,omitempty"`
	Requirements    *[]Requirement                  `` /* 127-byte string literal not displayed */
	Hints           []Requirement                   `yaml:"hints,omitempty" bson:"hints,omitempty" json:"hints,omitempty" mapstructure:"hints,omitempty"`
	Label           string                          `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
	Doc             string                          `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty" mapstructure:"doc,omitempty"`
	CwlVersion      CWLVersion                      `yaml:"cwlVersion,omitempty" bson:"cwlVersion,omitempty" json:"cwlVersion,omitempty" mapstructure:"cwlVersion,omitempty"`
}

http://www.commonwl.org/v1.0/Workflow.html#ExpressionTool

func NewExpressionTool added in v0.9.67 

func NewExpressionTool(original interface{}, CwlVersion CWLVersion, schemata []CWLType_Type) (et *ExpressionTool, err error)

TODO pass along workflow InlineJavascriptRequirement

type ExpressionToolOutputParameter added in v0.9.67 

type ExpressionToolOutputParameter struct {
	OutputParameter `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
}

http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter

func NewExpressionToolOutputParameter added in v0.9.67 

func NewExpressionToolOutputParameter(original interface{}, schemata []CWLType_Type) (wop *ExpressionToolOutputParameter, err error)

type File 

type File struct {
	CWLType_Impl `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // Provides: Id, Class, Type
	//Type           CWLType_Type  `yaml:"-" json:"-" bson:"-" mapstructure:"-"`
	Location       string        `yaml:"location,omitempty" json:"location,omitempty" bson:"location,omitempty" mapstructure:"location,omitempty"` // An IRI that identifies the file resource.
	Location_url   *url.URL      `yaml:"-" json:"-" bson:"-" mapstructure:"-"`                                                                     // only for internal purposes
	Path           string        `yaml:"path,omitempty" json:"path,omitempty" bson:"path,omitempty" mapstructure:"path,omitempty"`                 // dirname + '/' + basename == path This field must be set by the implementation.
	Basename       string        `yaml:"basename,omitempty" json:"basename,omitempty" bson:"basename,omitempty" mapstructure:"basename,omitempty"` // dirname + '/' + basename == path // if not defined, take from location
	Dirname        string        `yaml:"dirname,omitempty" json:"dirname,omitempty" bson:"dirname,omitempty" mapstructure:"dirname,omitempty"`     // dirname + '/' + basename == path
	Nameroot       string        `yaml:"nameroot,omitempty" json:"nameroot,omitempty" bson:"nameroot,omitempty" mapstructure:"nameroot,omitempty"`
	Nameext        string        `yaml:"nameext,omitempty" json:"nameext,omitempty" bson:"nameext,omitempty" mapstructure:"nameext,omitempty"`
	Checksum       string        `yaml:"checksum,omitempty" json:"checksum,omitempty" bson:"checksum,omitempty" mapstructure:"checksum,omitempty"`
	Size           int32         `yaml:"size,omitempty" json:"size,omitempty" bson:"size,omitempty" mapstructure:"size,omitempty"`
	SecondaryFiles []interface{} `` /* 135-byte string literal not displayed */
	Format         string        `yaml:"format,omitempty" json:"format,omitempty" bson:"format,omitempty" mapstructure:"format,omitempty"`
	Contents       string        `yaml:"contents,omitempty" json:"contents,omitempty" bson:"contents,omitempty" mapstructure:"contents,omitempty"`
	// Shock node
	Host   string `yaml:"-" json:"-" bson:"-" mapstructure:"-"`
	Node   string `yaml:"-" json:"-" bson:"-" mapstructure:"-"`
	Bearer string `yaml:"-" json:"-" bson:"-" mapstructure:"-"`
	Token  string `yaml:"-" json:"-" bson:"-" mapstructure:"-"`
}

http://www.commonwl.org/v1.0/Workflow.html#File

func MakeFile 

func MakeFile(obj interface{}) (file File, err error)

func NewFile added in v0.9.45 

func NewFile(obj interface{}) (file File, err error)

func (*File) GetType added in v0.9.62 

func (f *File) GetType() CWLType_Type

func (f *File) GetClass() string { return "File" }

func (*File) Is_CWLType added in v0.9.62 

func (f *File) Is_CWLType()

func (*File) Is_CWL_minimal added in v0.9.62 

func (f *File) Is_CWL_minimal()

func (*File) String 

func (f *File) String() string

func (f *File) GetId() string { return f.Id } func (f *File) SetId(id string) { f.Id = id }

type Float added in v0.9.62 

type Float float32

func NewFloat added in v0.9.62 

func NewFloat(value float32) *Float

func NewFloatFromInterface added in v0.9.62 

func NewFloatFromInterface(native interface{}) (i *Float, err error)

func NewFloatFromfloat32 added in v0.9.62 

func NewFloatFromfloat32(value float32) (i *Float)

func (*Float) GetClass added in v0.9.62 

func (i *Float) GetClass() string

func (*Float) GetId added in v0.9.62 

func (i *Float) GetId() string

func (*Float) GetType added in v0.9.62 

func (i *Float) GetType() CWLType_Type

func (*Float) Is_CWL_minimal added in v0.9.62 

func (i *Float) Is_CWL_minimal()

func (*Float) Is_CWL_object added in v0.9.67 

func (i *Float) Is_CWL_object()

func (*Float) SetId added in v0.9.62 

func (i *Float) SetId(x string)

func (*Float) String added in v0.9.62 

func (i *Float) String() string

type InitialWorkDirRequirement added in v0.9.62 

type InitialWorkDirRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
	Listing         []interface{} `yaml:"listing,omitempty" bson:"listing,omitempty" json:"listing,omitempty" mapstructure:"listing,omitempty"` // TODO: array<File | Directory | Dirent | string | Expression> | string | Expression
}

http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement

func NewInitialWorkDirRequirement added in v0.9.62 

func NewInitialWorkDirRequirement(original interface{}) (r *InitialWorkDirRequirement, err error)

func (InitialWorkDirRequirement) GetId added in v0.9.62 

func (c InitialWorkDirRequirement) GetId() string

type InlineJavascriptRequirement added in v0.9.62 

type InlineJavascriptRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
	ExpressionLib   []string `yaml:"expressionLib,omitempty" bson:"expressionLib,omitempty" json:"expressionLib,omitempty"`
}

func NewInlineJavascriptRequirement added in v0.9.62 

func NewInlineJavascriptRequirement() InlineJavascriptRequirement

func NewInlineJavascriptRequirementFromInterface added in v0.9.67 

func NewInlineJavascriptRequirementFromInterface(original interface{}) (r *InlineJavascriptRequirement, err error)

func (InlineJavascriptRequirement) GetId added in v0.9.62 

func (c InlineJavascriptRequirement) GetId() string

type InputArraySchema added in v0.9.62 

type InputArraySchema struct {
	ArraySchema  `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	InputBinding *CommandLineBinding `yaml:"inputBinding,omitempty" bson:"inputBinding,omitempty" json:"inputBinding,omitempty"`
}

func NewInputArraySchema added in v0.9.62 

func NewInputArraySchema() (coas *InputArraySchema)

func NewInputArraySchemaFromInterface added in v0.9.62 

func NewInputArraySchemaFromInterface(original interface{}, schemata []CWLType_Type) (coas *InputArraySchema, err error)

func (*InputArraySchema) GetId added in v0.9.67 

func (c *InputArraySchema) GetId() string

func (*InputArraySchema) Type2String added in v0.9.62 

func (c *InputArraySchema) Type2String() string

type InputEnumSchema added in v0.9.67 

type InputEnumSchema struct {
	EnumSchema   `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // provides Symbols, Type, Label
	InputBinding *CommandLineBinding                                                   `` /* 127-byte string literal not displayed */
}

func NewInputEnumSchemaFromInterface added in v0.9.67 

func NewInputEnumSchemaFromInterface(original interface{}) (ies *InputEnumSchema, err error)

type InputParameter 

type InputParameter struct {
	Id             string             `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty"`
	Label          string             `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty"`
	SecondaryFiles []string           `yaml:"secondaryFiles,omitempty" bson:"secondaryFiles,omitempty" json:"secondaryFiles,omitempty"` // TODO string | Expression | array<string | Expression>
	Format         []string           `yaml:"format,omitempty" bson:"format,omitempty" json:"format,omitempty"`
	Streamable     bool               `yaml:"streamable,omitempty" bson:"streamable,omitempty" json:"streamable,omitempty"`
	Doc            string             `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty"`
	InputBinding   CommandLineBinding `yaml:"inputBinding,omitempty" bson:"inputBinding,omitempty" json:"inputBinding,omitempty"` //TODO
	Default        CWLType            `yaml:"default,omitempty" bson:"default,omitempty" json:"default,omitempty"`
	Type           []CWLType_Type     `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty"` // TODO CWLType | InputRecordSchema | InputEnumSchema | InputArraySchema | string | array<CWLType | InputRecordSchema | InputEnumSchema | InputArraySchema | string>
}

func NewInputParameter added in v0.9.45 

func NewInputParameter(original interface{}, schemata []CWLType_Type) (input_parameter *InputParameter, err error)

func NewInputParameterArray added in v0.9.45 

func NewInputParameterArray(original interface{}, schemata []CWLType_Type) (new_array []InputParameter, err error)

InputParameter

func (InputParameter) GetClass 

func (i InputParameter) GetClass() string

func (InputParameter) GetId 

func (i InputParameter) GetId() string

func (InputParameter) Is_CWL_minimal added in v0.9.62 

func (i InputParameter) Is_CWL_minimal()

func (InputParameter) SetId 

func (i InputParameter) SetId(id string)

type InputParameterType added in v0.9.45 

type InputParameterType string

type InputRecordField added in v0.9.67 

type InputRecordField struct {
	RecordField `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#InputRecordField

func CreateInputRecordFieldArray added in v0.9.67 

func CreateInputRecordFieldArray(native []interface{}, schemata []CWLType_Type) (irfa []InputRecordField, err error)

func NewInputRecordField added in v0.9.67 

func NewInputRecordField(native interface{}, schemata []CWLType_Type) (irf *InputRecordField, err error)

type InputRecordSchema added in v0.9.67 

type InputRecordSchema struct {
	RecordSchema `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // provides Type, Label, Name
	Fields       []InputRecordField                                                    `yaml:"fields,omitempty" json:"fields,omitempty" bson:"fields,omitempty"`
	InputBinding *CommandLineBinding                                                   `yaml:"inputBinding,omitempty" json:"inputBinding,omitempty" bson:"inputBinding,omitempty"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#InputRecordSchema

func NewInputRecordSchema added in v0.9.67 

func NewInputRecordSchema(irs_map map[string]interface{}) (irs *InputRecordSchema, err error)

func NewInputRecordSchemaFromInterface added in v0.9.67 

func NewInputRecordSchemaFromInterface(native interface{}, schemata []CWLType_Type) (irs *InputRecordSchema, err error)

type Int 

type Int int

func NewInt added in v0.9.62 

func NewInt(value int) (i *Int)

func NewIntFromInterface added in v0.9.62 

func NewIntFromInterface(id string, native interface{}) (i *Int, err error)

func (*Int) GetClass 

func (i *Int) GetClass() string

func (*Int) GetId 

func (i *Int) GetId() string

func (*Int) GetType added in v0.9.62 

func (i *Int) GetType() CWLType_Type

func (*Int) Is_CWL_minimal added in v0.9.62 

func (i *Int) Is_CWL_minimal()

func (*Int) Is_CWL_object added in v0.9.67 

func (i *Int) Is_CWL_object()

func (*Int) SetId 

func (i *Int) SetId(x string)

func (*Int) String 

func (i *Int) String() string

type JobDocMap added in v0.9.62 

type JobDocMap map[string]CWLType

func (JobDocMap) GetArray added in v0.9.62 

func (jd_map JobDocMap) GetArray() (result Job_document, err error)

type Job_document 

type Job_document []NamedCWLType // JobDocArray

type Job_document map[string]interface{}

func NewJob_document added in v0.9.45 

func NewJob_document(original interface{}) (job *Job_document, err error)

func NewJob_documentFromNamedTypes added in v0.9.62 

func NewJob_documentFromNamedTypes(original interface{}) (job *Job_document, err error)

func ParseJob 

func ParseJob(job_byte_ptr *[]byte) (job_input *Job_document, err error)

func ParseJobFile added in v0.9.62 

func ParseJobFile(job_file string) (job_input *Job_document, err error)

func (*Job_document) GetMap added in v0.9.62 

func (job_input *Job_document) GetMap() (job_input_map JobDocMap)

type LinkMergeMethod 

type LinkMergeMethod string // merge_nested or merge_flattened

type Long added in v0.9.67 

type Long int64

func NewLong added in v0.9.67 

func NewLong(value int64) (i *Long)

func NewLongFromInterface added in v0.9.67 

func NewLongFromInterface(id string, native interface{}) (i *Long, err error)

func (*Long) GetClass added in v0.9.67 

func (i *Long) GetClass() string

func (*Long) GetId added in v0.9.67 

func (i *Long) GetId() string

func (*Long) GetType added in v0.9.67 

func (i *Long) GetType() CWLType_Type

func (*Long) Is_CWL_minimal added in v0.9.67 

func (i *Long) Is_CWL_minimal()

func (*Long) Is_CWL_object added in v0.9.67 

func (i *Long) Is_CWL_object()

func (*Long) SetId added in v0.9.67 

func (i *Long) SetId(x string)

func (*Long) String added in v0.9.67 

func (i *Long) String() string

type MultipleInputFeatureRequirement added in v0.9.62 

type MultipleInputFeatureRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
}

Indicates that the workflow platform must support multiple inbound data links listed in the source field of WorkflowStepInput.

func NewMultipleInputFeatureRequirement added in v0.9.62 

func NewMultipleInputFeatureRequirement(original interface{}) (r *MultipleInputFeatureRequirement, err error)

func (MultipleInputFeatureRequirement) GetId added in v0.9.62 

func (c MultipleInputFeatureRequirement) GetId() string

type NamedCWLType added in v0.9.62 

type NamedCWLType struct {
	CWL_id_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"` // provides id
	Value       CWLType                                                               `yaml:"value,omitempty" bson:"value,omitempty" json:"value,omitempty" mapstructure:"value,omitempty"`
}

func NewNamedCWLType added in v0.9.62 

func NewNamedCWLType(id string, value CWLType) NamedCWLType

func NewNamedCWLTypeFromInterface added in v0.9.62 

func NewNamedCWLTypeFromInterface(native interface{}) (cwl_obj_named NamedCWLType, err error)

type Named_CWL_object added in v0.9.67 

type Named_CWL_object struct {
	CWL_id_Impl `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"` // provides id
	Value       CWL_object                                                            `yaml:"value,omitempty" bson:"value,omitempty" json:"value,omitempty" mapstructure:"value,omitempty"`
}

func NewNamed_CWL_object added in v0.9.67 

func NewNamed_CWL_object(id string, value CWL_object) Named_CWL_object

type Named_CWL_object_array added in v0.9.67 

type Named_CWL_object_array []Named_CWL_object

type Null added in v0.9.62 

type Null string

func NewNull added in v0.9.62 

func NewNull() (n *Null)

func (*Null) GetBSON added in v0.9.67 

func (n *Null) GetBSON() (result interface{}, err error)

func (*Null) GetClass added in v0.9.62 

func (i *Null) GetClass() string

func (*Null) GetId added in v0.9.67 

func (i *Null) GetId() string

func (*Null) GetType added in v0.9.67 

func (i *Null) GetType() CWLType_Type

func (*Null) Is_CWL_minimal added in v0.9.67 

func (i *Null) Is_CWL_minimal()

func (*Null) Is_CWL_object added in v0.9.67 

func (i *Null) Is_CWL_object()

func (*Null) MarshalJSON added in v0.9.67 

func (n *Null) MarshalJSON() (b []byte, err error)

func (*Null) MarshalYAML added in v0.9.67 

func (n *Null) MarshalYAML() (i interface{}, err error)

No, use this: https://godoc.org/gopkg.in/yaml.v2#Marshaler

func (*Null) SetId added in v0.9.67 

func (i *Null) SetId(x string)

func (*Null) String added in v0.9.62 

func (i *Null) String() string

type Number added in v0.9.62 

type Number string

func NewNumber added in v0.9.62 

func NewNumber(id string, value string) (s *Number)

func NewNumberFromInterface added in v0.9.62 

func NewNumberFromInterface(id string, native interface{}) (s *Number, err error)

func NewNumberFromstring added in v0.9.62 

func NewNumberFromstring(value string) (s *Number)

func (*Number) GetClass added in v0.9.62 

func (s *Number) GetClass() string

func (*Number) GetId added in v0.9.62 

func (s *Number) GetId() string

func (*Number) GetType added in v0.9.62 

func (s *Number) GetType() CWLType_Type

func (*Number) Is_CWL_minimal added in v0.9.62 

func (s *Number) Is_CWL_minimal()

func (*Number) SetId added in v0.9.62 

func (s *Number) SetId(i string)

func (*Number) String added in v0.9.62 

func (s *Number) String() string

type OutputArraySchema added in v0.9.45 

type OutputArraySchema struct {
	ArraySchema   `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`
	OutputBinding *CommandOutputBinding `yaml:"outputBinding,omitempty" bson:"outputBinding,omitempty" json:"outputBinding,omitempty"`
}

func NewOutputArraySchema added in v0.9.62 

func NewOutputArraySchema() (coas *OutputArraySchema)

func NewOutputArraySchemaFromInterface added in v0.9.62 

func NewOutputArraySchemaFromInterface(original interface{}, schemata []CWLType_Type) (coas *OutputArraySchema, err error)

func (OutputArraySchema) GetId added in v0.9.67 

func (c OutputArraySchema) GetId() string

func (OutputArraySchema) Is_Type added in v0.9.67 

func (c OutputArraySchema) Is_Type()

func (OutputArraySchema) Type2String added in v0.9.62 

func (c OutputArraySchema) Type2String() string

type OutputEnumSchema added in v0.9.45 

type OutputEnumSchema struct{}

type OutputParameter added in v0.9.67 

type OutputParameter struct {
	Id             string                `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty"`
	Label          string                `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty"`
	SecondaryFiles []Expression          `yaml:"secondaryFiles,omitempty" bson:"secondaryFiles,omitempty" json:"secondaryFiles,omitempty"` // TODO string | Expression | array<string | Expression>
	Format         Expression            `yaml:"format,omitempty" bson:"format,omitempty" json:"format,omitempty"`
	Streamable     bool                  `yaml:"streamable,omitempty" bson:"streamable,omitempty" json:"streamable,omitempty"`
	OutputBinding  *CommandOutputBinding `yaml:"outputBinding,omitempty" bson:"outputBinding,omitempty" json:"outputBinding,omitempty"`
	Type           []interface{}         `yaml:"type,omitempty" bson:"type,omitempty" json:"type,omitempty"`
}

used for ExpressionToolOutputParameter, WorkflowOutputParameter, CommandOutputParameter

type OutputRecordSchema added in v0.9.45 

type OutputRecordSchema struct{}

type Pointer added in v0.9.67 

type Pointer string

func NewPointer added in v0.9.67 

func NewPointer(id string, value string) (s *Pointer)

func NewPointerFromInterface added in v0.9.67 

func NewPointerFromInterface(id string, native interface{}) (s *Pointer, err error)

func NewPointerFromstring added in v0.9.67 

func NewPointerFromstring(value string) (s *Pointer)

func (*Pointer) GetId added in v0.9.67 

func (s *Pointer) GetId() string

func (*Pointer) Is_Type added in v0.9.67 

func (c *Pointer) Is_Type()

func (s *Pointer) SetId(i string) {}

func (*Pointer) Type2String added in v0.9.67 

func (c *Pointer) Type2String() string

type Process added in v0.9.45 

type Process interface {
	CWL_object
	Is_process()
}

type ProcessPointer added in v0.9.45 

type ProcessPointer struct {
	Id    string
	Value string
}

func NewProcessPointer added in v0.9.62 

func NewProcessPointer(original interface{}) (pp *ProcessPointer, err error)

func (*ProcessPointer) GetClass added in v0.9.45 

func (p *ProcessPointer) GetClass() string

func (*ProcessPointer) GetId added in v0.9.45 

func (p *ProcessPointer) GetId() string

func (*ProcessPointer) Is_CWL_minimal added in v0.9.62 

func (p *ProcessPointer) Is_CWL_minimal()

func (*ProcessPointer) Is_process added in v0.9.62 

func (p *ProcessPointer) Is_process()

func (*ProcessPointer) SetId added in v0.9.45 

func (p *ProcessPointer) SetId(string)

type Record added in v0.9.62 

type Record map[string]CWLType

func NewRecord added in v0.9.62 

func NewRecord(id string, native interface{}) (record Record, err error)

func (*Record) GetClass added in v0.9.62 

func (r *Record) GetClass() string

func (*Record) GetId added in v0.9.67 

func (r *Record) GetId() string

func (*Record) GetType added in v0.9.67 

func (r *Record) GetType() CWLType_Type

func (*Record) Is_CWL_minimal added in v0.9.62 

func (r *Record) Is_CWL_minimal()

func (*Record) Is_CWL_object added in v0.9.67 

func (r *Record) Is_CWL_object()

func (*Record) Is_Type added in v0.9.67 

func (r *Record) Is_Type()

func (*Record) SetId added in v0.9.67 

func (r *Record) SetId(id string)

func (Record) String added in v0.9.62 

func (c Record) String() string

func (*Record) Type2String added in v0.9.67 

func (r *Record) Type2String() string

type RecordField added in v0.9.67 

type RecordField struct {
	Name         string              `yaml:"name,omitempty" json:"name,omitempty" bson:"name,omitempty"`
	Type         []CWLType_Type      `yaml:"type,omitempty" json:"type,omitempty" bson:"type,omitempty"` // CWLType | InputRecordSchema | InputEnumSchema | InputArraySchema | string | array<CWLType | InputRecordSchema | InputEnumSchema | InputArraySchema | string>
	Doc          string              `yaml:"doc,omitempty" json:"doc,omitempty" bson:"doc,omitempty"`
	InputBinding *CommandLineBinding `yaml:"inputBinding,omitempty" json:"inputBinding,omitempty" bson:"inputBinding,omitempty"`
	Label        string              `yaml:"label,omitempty" json:"label,omitempty" bson:"label,omitempty"`
}

http://www.commonwl.org/v1.0/CommandLineTool.html#InputRecordField

func NewRecordFieldFromInterface added in v0.9.67 

func NewRecordFieldFromInterface(native interface{}, schemata []CWLType_Type) (rf *RecordField, err error)

type RecordSchema added in v0.9.67 

type RecordSchema struct {
	Type  CWLType_Type `yaml:"type,omitempty" json:"type,omitempty" bson:"type,omitempty"`
	Label string       `yaml:"label,omitempty" json:"label,omitempty" bson:"label,omitempty"`
	Name  string       `yaml:"name,omitempty" json:"name,omitempty" bson:"name,omitempty"`
}

func NewRecordSchema added in v0.9.67 

func NewRecordSchema(native_map map[string]interface{}) (rs *RecordSchema, err error)

func (*RecordSchema) GetId added in v0.9.67 

func (r *RecordSchema) GetId() string

func (*RecordSchema) Is_Type added in v0.9.67 

func (r *RecordSchema) Is_Type()

func (*RecordSchema) Type2String added in v0.9.67 

func (r *RecordSchema) Type2String() string

type Requirement 

type Requirement interface {
	GetClass() string
}

func GetRequirement added in v0.9.67 

func GetRequirement(r_name string, array_ptr *[]Requirement) (requirement *Requirement, err error)

type ResourceRequirement added in v0.9.67 

type ResourceRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
	CoresMin        int `yaml:"coresMin,omitempty" bson:"coresMin,omitempty" json:"coresMin,omitempty"`
	CoresMax        int `yaml:"coresMax,omitempty" bson:"coresMax,omitempty" json:"coresMax,omitempty"`
	RamMin          int `yaml:"ramMin,omitempty" bson:"ramMin,omitempty" json:"ramMin,omitempty"`
	RamMax          int `yaml:"ramMax,omitempty" bson:"ramMax,omitempty" json:"ramMax,omitempty"`
	TmpdirMin       int `yaml:"tmpdirMin,omitempty" bson:"tmpdirMin,omitempty" json:"tmpdirMin,omitempty"`
	TmpdirMax       int `yaml:"tmpdirMax,omitempty" bson:"tmpdirMax,omitempty" json:"tmpdirMax,omitempty"`
	OutdirMin       int `yaml:"outdirMin,omitempty" bson:"outdirMin,omitempty" json:"outdirMin,omitempty"`
	OutdirMax       int `yaml:"outdirMax,omitempty" bson:"outdirMax,omitempty" json:"outdirMax,omitempty"`
}

func NewResourceRequirement added in v0.9.67 

func NewResourceRequirement(original interface{}) (r *ResourceRequirement, err error)

func (ResourceRequirement) GetId added in v0.9.67 

func (c ResourceRequirement) GetId() string

type ScatterFeatureRequirement added in v0.9.62 

type ScatterFeatureRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
}

Indicates that the workflow platform must support the scatter and scatterMethod fields of WorkflowStep.

func NewScatterFeatureRequirement added in v0.9.62 

func NewScatterFeatureRequirement(original interface{}) (r *ScatterFeatureRequirement, err error)

func (ScatterFeatureRequirement) GetId added in v0.9.62 

func (c ScatterFeatureRequirement) GetId() string

type SchemaDefRequirement added in v0.9.67 

type SchemaDefRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
	Types           []interface{} `yaml:"types,omitempty" json:"types,omitempty" bson:"types,omitempty"` // array<InputRecordSchema | InputEnumSchema | InputArraySchema>
}

http://www.commonwl.org/v1.0/Workflow.html#SchemaDefRequirement

func (SchemaDefRequirement) GetId added in v0.9.67 

func (c SchemaDefRequirement) GetId() string

type ShellCommandRequirement added in v0.9.67 

type ShellCommandRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
}

https://www.commonwl.org/v1.0/CommandLineTool.html#ShellCommandRequirement

func NewShellCommandRequirement added in v0.9.67 

func NewShellCommandRequirement(original interface{}) (r *ShellCommandRequirement, err error)

func (ShellCommandRequirement) GetId added in v0.9.67 

func (c ShellCommandRequirement) GetId() string

type ShockRequirement 

type ShockRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" `
	Shock_api_url   string `` /* 131-byte string literal not displayed */
}

func GetShockRequirement added in v0.9.67 

func GetShockRequirement(array_ptr *[]Requirement) (shock_requirement *ShockRequirement, err error)

func NewShockRequirement added in v0.9.62 

func NewShockRequirement(url string) (requirement_ptr *ShockRequirement, err error)

func NewShockRequirementFromInterface added in v0.9.67 

func NewShockRequirementFromInterface(original interface{}) (r *ShockRequirement, err error)

func (ShockRequirement) GetId 

func (s ShockRequirement) GetId() string

type StepInputExpressionRequirement 

type StepInputExpressionRequirement struct {
	BaseRequirement `bson:",inline" yaml:",inline" json:",inline" mapstructure:",squash"`
}

http://www.commonwl.org/v1.0/Workflow.html#StepInputExpressionRequirement

func NewStepInputExpressionRequirement added in v0.9.62 

func NewStepInputExpressionRequirement(original interface{}) (r *StepInputExpressionRequirement, err error)

func (StepInputExpressionRequirement) GetId 

func (c StepInputExpressionRequirement) GetId() string

type String 

type String string

func NewString added in v0.9.62 

func NewString(value string) (s *String)

func NewStringFromInterface added in v0.9.62 

func NewStringFromInterface(native interface{}) (s *String, err error)

func (*String) GetClass 

func (s *String) GetClass() string

func (*String) GetId 

func (s *String) GetId() string

func (*String) GetType added in v0.9.62 

func (s *String) GetType() CWLType_Type

func (*String) Is_CWL_minimal added in v0.9.62 

func (s *String) Is_CWL_minimal()

func (*String) Is_CWL_object added in v0.9.67 

func (s *String) Is_CWL_object()

func (*String) SetId 

func (s *String) SetId(i string)

func (*String) String 

func (s *String) String() string

type Workflow 

type Workflow struct {
	CWL_object_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"`
	CWL_class_Impl  `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"` // provides Id and Class fields
	CWL_id_Impl     `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"`
	Inputs          []InputParameter          `yaml:"inputs,omitempty" bson:"inputs,omitempty" json:"inputs,omitempty" mapstructure:"inputs,omitempty"`
	Outputs         []WorkflowOutputParameter `yaml:"outputs,omitempty" bson:"outputs,omitempty" json:"outputs,omitempty" mapstructure:"outputs,omitempty"`
	Steps           []WorkflowStep            `yaml:"steps,omitempty" bson:"steps,omitempty" json:"steps,omitempty" mapstructure:"steps,omitempty"`
	Requirements    *[]Requirement            `` //[]Requirement
	/* 127-byte string literal not displayed */
	Hints      []interface{}          `yaml:"hints,omitempty" bson:"hints,omitempty" json:"hints,omitempty" mapstructure:"hints,omitempty"` // []Requirement TODO Hints may contain non-requirement objects. Give warning in those cases.
	Label      string                 `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
	Doc        string                 `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty" mapstructure:"doc,omitempty"`
	CwlVersion CWLVersion             `yaml:"cwlVersion,omitempty" bson:"cwlVersion,omitempty" json:"cwlVersion,omitempty" mapstructure:"cwlVersion,omitempty"`
	Metadata   map[string]interface{} `yaml:"metadata,omitempty" bson:"metadata,omitempty" json:"metadata,omitempty" mapstructure:"metadata,omitempty"`
}

func NewWorkflowEmpty added in v0.9.67 

func NewWorkflowEmpty() (w Workflow)

func (*Workflow) GetClass 

func (w *Workflow) GetClass() string

func (*Workflow) Is_process added in v0.9.62 

func (w *Workflow) Is_process()

func (w *Workflow) GetId() string { return w.Id } func (w *Workflow) SetId(id string) { w.Id = id } func (w *Workflow) Is_CWL_minimal() {} func (w *Workflow) Is_Any() {}

type WorkflowOutputParameter 

type WorkflowOutputParameter struct {
	OutputParameter `yaml:",inline" json:",inline" bson:",inline" mapstructure:",squash"`

	Doc string `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty"`
	//OutputBinding  *CommandOutputBinding `yaml:"outputBinding,omitempty" bson:"outputBinding,omitempty" json:"outputBinding,omitempty"` //TODO
	OutputSource interface{}     `yaml:"outputSource,omitempty" bson:"outputSource,omitempty" json:"outputSource,omitempty"` //string or []string
	LinkMerge    LinkMergeMethod `yaml:"linkMerge,omitempty" bson:"linkMerge,omitempty" json:"linkMerge,omitempty"`
}

func NewWorkflowOutputParameter added in v0.9.45 

func NewWorkflowOutputParameter(original interface{}, schemata []CWLType_Type) (wop *WorkflowOutputParameter, err error)

type WorkflowStep 

type WorkflowStep struct {
	Id           string               `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty" mapstructure:"id,omitempty"`
	In           []WorkflowStepInput  `yaml:"in,omitempty" bson:"in,omitempty" json:"in,omitempty" mapstructure:"in,omitempty"` // array<WorkflowStepInput> | map<WorkflowStepInput.id, WorkflowStepInput.source> | map<WorkflowStepInput.id, WorkflowStepInput>
	Out          []WorkflowStepOutput `yaml:"out,omitempty" bson:"out,omitempty" json:"out,omitempty" mapstructure:"out,omitempty"`
	Run          interface{}          `yaml:"run,omitempty" bson:"run,omitempty" json:"run,omitempty" mapstructure:"run,omitempty"` // (*Process) Specification unclear: string | CommandLineTool | ExpressionTool | Workflow
	Requirements []interface{}        ``                                                                                            //[]Requirement
	/* 127-byte string literal not displayed */
	Hints         []interface{} `yaml:"hints,omitempty" bson:"hints,omitempty" json:"hints,omitempty" mapstructure:"hints,omitempty"` //[]Requirement
	Label         string        `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
	Doc           string        `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty" mapstructure:"doc,omitempty"`
	Scatter       []string      `yaml:"scatter,omitempty" bson:"scatter,omitempty" json:"scatter,omitempty" mapstructure:"scatter,omitempty"` // ScatterFeatureRequirement
	ScatterMethod string        ``                                                                                                            // ScatterFeatureRequirement
	/* 131-byte string literal not displayed */
}

func (WorkflowStep) GetOutput 

func (w WorkflowStep) GetOutput(id string) (output *WorkflowStepOutput, err error)

type WorkflowStepInput 

type WorkflowStepInput struct {
	CWL_object_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"`
	Id              string           `yaml:"id,omitempty" bson:"id,omitempty" json:"id,omitempty" mapstructure:"id,omitempty"`
	Source          interface{}      `yaml:"source,omitempty" bson:"source,omitempty" json:"source,omitempty" mapstructure:"source,omitempty"` // MultipleInputFeatureRequirement
	LinkMerge       *LinkMergeMethod `yaml:"linkMerge,omitempty" bson:"linkMerge,omitempty" json:"linkMerge,omitempty" mapstructure:"linkMerge,omitempty"`
	Default         interface{}      `yaml:"default,omitempty" bson:"default,omitempty" json:"default,omitempty" mapstructure:"default,omitempty"`         // type Any does not make sense
	ValueFrom       Expression       `yaml:"valueFrom,omitempty" bson:"valueFrom,omitempty" json:"valueFrom,omitempty" mapstructure:"valueFrom,omitempty"` // StepInputExpressionRequirement
	Ready           bool             `yaml:"-" bson:"-" json:"-" mapstructure:"-"`
}

http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput

func NewWorkflowStepInput added in v0.9.45 

func NewWorkflowStepInput(original interface{}) (input_parameter_ptr *WorkflowStepInput, err error)

func (WorkflowStepInput) GetClass 

func (w WorkflowStepInput) GetClass() string

func (WorkflowStepInput) GetId 

func (w WorkflowStepInput) GetId() string

func (WorkflowStepInput) Is_CWL_minimal added in v0.9.62 

func (w WorkflowStepInput) Is_CWL_minimal()

func (WorkflowStepInput) SetId 

func (w WorkflowStepInput) SetId(id string)

type WorkflowStepOutput 

type WorkflowStepOutput struct {
	Id string `yaml:"id" bson:"id" json:"id" mapstructure:"id"`
}

func NewWorkflowStepOutput added in v0.9.62 

func NewWorkflowStepOutput(original interface{}) (wso_ptr *WorkflowStepOutput, err error)

func NewWorkflowStepOutputArray added in v0.9.62 

func NewWorkflowStepOutputArray(original interface{}) (new_array []WorkflowStepOutput, err error)

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.