Index (dockstore-galaxy-interface 0.0.9-SNAPSHOT API)

A B C D E F G H I L M N O P Q R S T U V W Y
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

Any - Enum Class in org.galaxyproject.gxformat2.v19_09
Any - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
ANY - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.Any
AnyInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
AnyLoader - Class in org.galaxyproject.gxformat2.v19_09.utils
AnyLoader() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.AnyLoader
ARRAY - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.enum_d062602be0b4b8fd33e69e29a841317b6ab665bc
array_of_GalaxyWorkflow - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_RecordField - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_union_of_StringInstance_or_WorkflowStepOutput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_WorkflowInputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_WorkflowOutputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_WorkflowStep - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
array_of_WorkflowStepInput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
ArrayLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
ArrayLoader(Loader<T>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.ArrayLoader
ArraySchema - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/salad#ArraySchema
This interface is implemented by ArraySchemaImpl
ArraySchema - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
ArraySchemaImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema
ArraySchemaImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.ArraySchemaImpl: Used by RootLoader to construct instances of ArraySchemaImpl.

B

BOOLEAN - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
BooleanInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
build() - Method in class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder

C

COLLECTION - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType
collectMessages() - Method in class org.galaxyproject.gxformat2.LintContext
ConstantMaps - Class in org.galaxyproject.gxformat2.v19_09.utils
ConstantMaps() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.ConstantMaps
copiedFrom(LoadingOptions) - Method in class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder
Cytoscape - Class in org.galaxyproject.gxformat2: General notes: There's no guarantee that a normalized step has a label, step definition ID or state
Cytoscape() - Constructor for class org.galaxyproject.gxformat2.Cytoscape
CytoscapeDAG - Class in org.galaxyproject.gxformat2
CytoscapeDAG() - Constructor for class org.galaxyproject.gxformat2.CytoscapeDAG
CytoscapeDAG.Edge - Class in org.galaxyproject.gxformat2
CytoscapeDAG.Edge.EdgeData - Class in org.galaxyproject.gxformat2
CytoscapeDAG.Node - Class in org.galaxyproject.gxformat2
CytoscapeDAG.Node.NodeData - Class in org.galaxyproject.gxformat2

D

DATA - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType
DefaultFetcher - Class in org.galaxyproject.gxformat2.v19_09.utils
DefaultFetcher() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.DefaultFetcher
Documented - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/salad#Documented
Documented - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
documentLoad(String, String, LoadingOptions) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
documentLoad(List<Object>, String, LoadingOptions) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
documentLoad(Map<String, Object>, String, LoadingOptions) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
documentLoadByUrl(String, LoadingOptions) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
DOUBLE - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
DoubleInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances

E

Edge() - Constructor for class org.galaxyproject.gxformat2.CytoscapeDAG.Edge
EdgeData() - Constructor for class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
END_ID - Static variable in class org.galaxyproject.gxformat2.Cytoscape
ensurePosition(Map<String, Object>, int) - Method in interface org.galaxyproject.gxformat2.WorkflowAdapter
ENUM - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.enum_d961d79c225752b9fadb617367615ab176b47d77
enum_d062602be0b4b8fd33e69e29a841317b6ab665bc - Enum Class in org.galaxyproject.gxformat2.v19_09
enum_d062602be0b4b8fd33e69e29a841317b6ab665bc - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
enum_d961d79c225752b9fadb617367615ab176b47d77 - Enum Class in org.galaxyproject.gxformat2.v19_09
enum_d961d79c225752b9fadb617367615ab176b47d77 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
enum_d9cba076fca539106791a4f46d198c7fcfbdb779 - Enum Class in org.galaxyproject.gxformat2.v19_09
enum_d9cba076fca539106791a4f46d198c7fcfbdb779 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
EnumLoader<T extends Enum> - Class in org.galaxyproject.gxformat2.v19_09.utils
EnumLoader(Class<T>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.EnumLoader
EnumSchema - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/salad#EnumSchema
This interface is implemented by EnumSchemaImpl
Define an enumerated type.
EnumSchema - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
EnumSchemaImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://w3id.org/cwl/salad#EnumSchema
Define an enumerated type.
EnumSchemaImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.EnumSchemaImpl: Used by RootLoader to construct instances of EnumSchemaImpl.
EXIT_CODE_FILE_PARSE_FAILED - Static variable in class org.galaxyproject.gxformat2.Lint
EXIT_CODE_FORMAT_ERROR - Static variable in class org.galaxyproject.gxformat2.Lint
EXIT_CODE_LINT_FAILED - Static variable in class org.galaxyproject.gxformat2.Lint
EXIT_CODE_SUCCESS - Static variable in class org.galaxyproject.gxformat2.Lint
expandUrl(String, String, boolean, boolean, Integer) - Method in class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions

F

Fetcher - Interface in org.galaxyproject.gxformat2.v19_09.utils
fetchText(String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.DefaultFetcher
fetchText(String) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Fetcher
FILE - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType
fileUri(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris
fileUri(String, boolean) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris
findTestParameterFile(String, MinimalLanguageInterface.FileReader) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
FLOAT - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
FloatInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
Format2Linter - Class in org.galaxyproject.gxformat2
Format2Linter() - Constructor for class org.galaxyproject.gxformat2.Format2Linter
Format2WorkflowAdapter - Class in org.galaxyproject.gxformat2
Format2WorkflowAdapter(Map<String, Object>) - Constructor for class org.galaxyproject.gxformat2.Format2WorkflowAdapter
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.Any
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d062602be0b4b8fd33e69e29a841317b6ab665bc
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d961d79c225752b9fadb617367615ab176b47d77
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d9cba076fca539106791a4f46d198c7fcfbdb779
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
fromDocumentVal(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.WorkflowStepType

G

GalaxyType - Enum Class in org.galaxyproject.gxformat2.v19_09
GalaxyType - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
GalaxyWorkflow - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow
This interface is implemented by GalaxyWorkflowImpl
A Galaxy workflow description.
GalaxyWorkflow - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
GalaxyWorkflowImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow
A Galaxy workflow description.
GalaxyWorkflowImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Used by RootLoader to construct instances of GalaxyWorkflowImpl.
GalaxyWorkflowLinter - Interface in org.galaxyproject.gxformat2
GalaxyWorkflowPlugin - Class in org.galaxyproject.dockstore_galaxy_interface.language
GalaxyWorkflowPlugin(PluginWrapper) - Constructor for class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin: Constructor to be used by plugin manager for plugin instantiation.
GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl - Class in org.galaxyproject.dockstore_galaxy_interface.language
GalaxyWorkflowPluginImpl() - Constructor for class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
generateToolsTable(String, String, Map<String, MinimalLanguageInterface.FileMetadata>) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
getAdd_tags() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/add_tags
getAdd_tags() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/add_tags
getChange_datatype() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/change_datatype
getChange_datatype() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/change_datatype
getChangeset_revision() - Method in interface org.galaxyproject.gxformat2.v19_09.ToolShedRepository: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/changeset_revision
The revision of the tool shed repository this tool can be found in.
getChangeset_revision() - Method in class org.galaxyproject.gxformat2.v19_09.ToolShedRepositoryImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/changeset_revision
The revision of the tool shed repository this tool can be found in.
getClass_() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/class
getClass_() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/class
getData() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge
getData() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node
getDefault() - Method in interface org.galaxyproject.gxformat2.v19_09.InputParameter: Getter for property https://w3id.org/cwl/salad#default
The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`.
getDefault() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowInputParameter: Getter for property https://w3id.org/cwl/salad#default
The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`.
getDefault() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowInputParameterImpl: Getter for property https://w3id.org/cwl/salad#default
The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`.
getDefault() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepInput: Getter for property https://w3id.org/cwl/salad#default
The default value for this parameter to use if either there is no `source` field, or the value produced by the `source` is `null`.
getDefault() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepInputImpl: Getter for property https://w3id.org/cwl/salad#default
The default value for this parameter to use if either there is no `source` field, or the value produced by the `source` is `null`.
getDelete_intermediate_datasets() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/delete_intermediate_datasets
getDelete_intermediate_datasets() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/delete_intermediate_datasets
getDescriptorLanguage() - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.Documented: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: 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.
getDoc() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.InputParameter: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.OutputParameter: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.Parameter: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.Process: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.RecordField: 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.
getDoc() - Method in class org.galaxyproject.gxformat2.v19_09.RecordFieldImpl: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowInputParameter: 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.
getDoc() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowInputParameterImpl: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameter: 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.
getDoc() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameterImpl: 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.
getDoc() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: 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.
getDoc() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: 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.
getDocker() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
getEdges() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG
getElements(String) - Static method in class org.galaxyproject.gxformat2.Cytoscape
getElements(Map<String, Object>) - Static method in class org.galaxyproject.gxformat2.Cytoscape
getErrors() - Method in interface org.galaxyproject.gxformat2.v19_09.HasStepErrors: 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..
getErrors() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: 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..
getErrors() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: 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..
getFields() - Method in interface org.galaxyproject.gxformat2.v19_09.RecordSchema: Getter for property https://w3id.org/cwl/salad#fields
Defines the fields of the record.
getFields() - Method in class org.galaxyproject.gxformat2.v19_09.RecordSchemaImpl: Getter for property https://w3id.org/cwl/salad#fields
Defines the fields of the record.
getFoundErrors() - Method in class org.galaxyproject.gxformat2.LintContext
getFoundWarns() - Method in class org.galaxyproject.gxformat2.LintContext
getHide() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/hide
getHide() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/hide
getId() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
getId() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
getId() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowInputParameter: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowInputParameterImpl: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameter: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameterImpl: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepInput: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepInputImpl: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getId() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://w3id.org/cwl/cwl#Identified/id
The unique identifier for this object.
getIn() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/v19_09#in
Defines the input parameters of the workflow step.
getIn() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#in
Defines the input parameters of the workflow step.
getInputs() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://w3id.org/cwl/cwl#inputs
Defines the input parameters of the process.
getInputs() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://w3id.org/cwl/cwl#inputs
Defines the input parameters of the process.
getInputs() - Method in interface org.galaxyproject.gxformat2.v19_09.Process: Getter for property https://w3id.org/cwl/cwl#inputs
Defines the input parameters of the process.
getItems() - Method in interface org.galaxyproject.gxformat2.v19_09.ArraySchema: Getter for property https://w3id.org/cwl/salad#items
Defines the type of the array elements.
getItems() - Method in class org.galaxyproject.gxformat2.v19_09.ArraySchemaImpl: Getter for property https://w3id.org/cwl/salad#items
Defines the type of the array elements.
getLabel() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in interface org.galaxyproject.gxformat2.v19_09.Labeled: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in interface org.galaxyproject.gxformat2.v19_09.Process: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepInput: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLabel() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepInputImpl: Getter for property https://w3id.org/cwl/cwl#Labeled/label
A short, human-readable label of this object.
getLeft() - Method in interface org.galaxyproject.gxformat2.v19_09.StepPosition: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#StepPosition/left
Relative horizontal position of the step's node when rendered in the workflow editor.
getLeft() - Method in class org.galaxyproject.gxformat2.v19_09.StepPositionImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#StepPosition/left
Relative horizontal position of the step's node when rendered in the workflow editor.
getList() - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
getListOptional() - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
getMarkdown() - Method in interface org.galaxyproject.gxformat2.v19_09.Report: Getter for property https://galaxyproject.org/gxformat2/v19_09#Report/markdown
Galaxy flavored Markdown to define an invocation report.
getMarkdown() - Method in class org.galaxyproject.gxformat2.v19_09.ReportImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#Report/markdown
Galaxy flavored Markdown to define an invocation report.
getMessage() - Method in exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
getName() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
getName() - Method in interface org.galaxyproject.gxformat2.v19_09.RecordField: Getter for property https://w3id.org/cwl/salad#RecordField/name
The name of the field *
getName() - Method in class org.galaxyproject.gxformat2.v19_09.RecordFieldImpl: Getter for property https://w3id.org/cwl/salad#RecordField/name
The name of the field *
getName() - Method in interface org.galaxyproject.gxformat2.v19_09.ToolShedRepository: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/name
The name of the tool shed repository this tool can be found in.
getName() - Method in class org.galaxyproject.gxformat2.v19_09.ToolShedRepositoryImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/name
The name of the tool shed repository this tool can be found in.
getNodes() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG
getOne() - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
getOneOptional() - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
getOut() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/v19_09#out
Defines the parameters representing the output of the process.
getOut() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#out
Defines the parameters representing the output of the process.
getOutputs() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://w3id.org/cwl/cwl#outputs
Defines the parameters representing the output of the process.
getOutputs() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://w3id.org/cwl/cwl#outputs
Defines the parameters representing the output of the process.
getOutputs() - Method in interface org.galaxyproject.gxformat2.v19_09.Process: Getter for property https://w3id.org/cwl/cwl#outputs
Defines the parameters representing the output of the process.
getOutputSource() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameter: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter/outputSource
Specifies workflow parameter that supply the value of to the output parameter.
getOutputSource() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameterImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter/outputSource
Specifies workflow parameter that supply the value of to the output parameter.
getOwner() - Method in interface org.galaxyproject.gxformat2.v19_09.ToolShedRepository: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/owner
The owner of the tool shed repository this tool can be found in.
getOwner() - Method in class org.galaxyproject.gxformat2.v19_09.ToolShedRepositoryImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/owner
The owner of the tool shed repository this tool can be found in.
getPosition() - Method in interface org.galaxyproject.gxformat2.v19_09.HasStepPosition: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
getPosition() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowInputParameter: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
getPosition() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowInputParameterImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
getPosition() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
getPosition() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
getRemove_tags() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/remove_tags
getRemove_tags() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/remove_tags
getRename() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/rename
getRename() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/rename
getReport() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/report
Workflow invocation report template.
getReport() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/report
Workflow invocation report template.
getRun() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
getRun() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://w3id.org/cwl/cwl#run
Specifies a subworkflow to run.
getRun() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://w3id.org/cwl/cwl#run
Specifies a subworkflow to run.
getRuntime_inputs() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStep/runtime_inputs
getRuntime_inputs() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStep/runtime_inputs
getSet_columns() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepOutput: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/set_columns
getSet_columns() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput/set_columns
getSource() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
getSource() - Method in interface org.galaxyproject.gxformat2.v19_09.Sink: Getter for property https://w3id.org/cwl/cwl#source
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
getSource() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStepInput: Getter for property https://w3id.org/cwl/cwl#source
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
getSource() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepInputImpl: Getter for property https://w3id.org/cwl/cwl#source
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
getState() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/v19_09#state
Structured tool state.
getState() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#state
Structured tool state.
getSteps() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/steps
The individual steps that make up the workflow.
getSteps() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/steps
The individual steps that make up the workflow.
getSymbols() - Method in interface org.galaxyproject.gxformat2.v19_09.EnumSchema: Getter for property https://w3id.org/cwl/salad#symbols
Defines the set of valid symbols.
getSymbols() - Method in class org.galaxyproject.gxformat2.v19_09.EnumSchemaImpl: Getter for property https://w3id.org/cwl/salad#symbols
Defines the set of valid symbols.
getTarget() - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
getTool_id() - Method in interface org.galaxyproject.gxformat2.v19_09.ReferencesTool: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
The tool ID used to run this step of the workflow (e.g.
getTool_id() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
The tool ID used to run this step of the workflow (e.g.
getTool_id() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
The tool ID used to run this step of the workflow (e.g.
getTool_shed() - Method in interface org.galaxyproject.gxformat2.v19_09.ToolShedRepository: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/tool_shed
The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu.
getTool_shed() - Method in class org.galaxyproject.gxformat2.v19_09.ToolShedRepositoryImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository/tool_shed
The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu.
getTool_shed_repository() - Method in interface org.galaxyproject.gxformat2.v19_09.ReferencesTool: 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.
getTool_shed_repository() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: 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.
getTool_shed_repository() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: 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.
getTool_state() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/v19_09#tool_state
Unstructured tool state.
getTool_state() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/v19_09#tool_state
Unstructured tool state.
getTool_version() - Method in interface org.galaxyproject.gxformat2.v19_09.ReferencesTool: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
The tool version corresponding used to run this step of the workflow.
getTool_version() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
The tool version corresponding used to run this step of the workflow.
getTool_version() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
The tool version corresponding used to run this step of the workflow.
getTop() - Method in interface org.galaxyproject.gxformat2.v19_09.StepPosition: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#StepPosition/top
Relative vertical position of the step's node when rendered in the workflow editor.
getTop() - Method in class org.galaxyproject.gxformat2.v19_09.StepPositionImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#StepPosition/top
Relative vertical position of the step's node when rendered in the workflow editor.
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.ArraySchema: Getter for property https://w3id.org/cwl/salad#type
Must be `array` *
getType() - Method in class org.galaxyproject.gxformat2.v19_09.ArraySchemaImpl: Getter for property https://w3id.org/cwl/salad#type
Must be `array` *
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.EnumSchema: Getter for property https://w3id.org/cwl/salad#type
Must be `enum` *
getType() - Method in class org.galaxyproject.gxformat2.v19_09.EnumSchemaImpl: Getter for property https://w3id.org/cwl/salad#type
Must be `enum` *
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.RecordField: Getter for property https://w3id.org/cwl/salad#type
The field type *
getType() - Method in class org.galaxyproject.gxformat2.v19_09.RecordFieldImpl: Getter for property https://w3id.org/cwl/salad#type
The field type *
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.RecordSchema: Getter for property https://w3id.org/cwl/salad#type
Must be `record` *
getType() - Method in class org.galaxyproject.gxformat2.v19_09.RecordSchemaImpl: Getter for property https://w3id.org/cwl/salad#type
Must be `record` *
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowInputParameter: Getter for property https://w3id.org/cwl/salad#type
Specify valid types of data that may be assigned to this parameter.
getType() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowInputParameterImpl: Getter for property https://w3id.org/cwl/salad#type
Specify valid types of data that may be assigned to this parameter.
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameter: Getter for property https://w3id.org/cwl/salad#type
Specify valid types of data that may be assigned to this parameter.
getType() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameterImpl: Getter for property https://w3id.org/cwl/salad#type
Specify valid types of data that may be assigned to this parameter.
getType() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://w3id.org/cwl/salad#type
Workflow step module's type (defaults to 'tool').
getType() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://w3id.org/cwl/salad#type
Workflow step module's type (defaults to 'tool').
getUuid() - Method in interface org.galaxyproject.gxformat2.v19_09.GalaxyWorkflow: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
UUID uniquely representing this element.
getUuid() - Method in class org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
UUID uniquely representing this element.
getUuid() - Method in interface org.galaxyproject.gxformat2.v19_09.HasUUID: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
UUID uniquely representing this element.
getUuid() - Method in interface org.galaxyproject.gxformat2.v19_09.WorkflowStep: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
UUID uniquely representing this element.
getUuid() - Method in class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
UUID uniquely representing this element.

H

HasStepErrors - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors
HasStepErrors - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
HasStepPosition - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition
HasStepPosition - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
HasUUID - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasUUID
HasUUID - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances

I

Identified - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/cwl#Identified
Identified - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
idmap_fields_optional_array_of_RecordField - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
idmap_in_optional_array_of_WorkflowStepInput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
idmap_inputs_array_of_WorkflowInputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
idmap_out_optional_array_of_union_of_StringInstance_or_WorkflowStepOutput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
idmap_outputs_array_of_WorkflowOutputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
idmap_steps_array_of_WorkflowStep - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
IdMapLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
IdMapLoader(Loader<T>, String, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.IdMapLoader
indexWorkflowFiles(String, String, MinimalLanguageInterface.FileReader) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
initialPathPattern() - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
Input() - Constructor for class org.galaxyproject.gxformat2.WorkflowAdapter.Input
InputParameter - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter
InputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
INT - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
INTEGER - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType
IntegerInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
IoUtils - Class in org.galaxyproject.gxformat2
IoUtils() - Constructor for class org.galaxyproject.gxformat2.IoUtils
isGXFormat2Workflow(Map<String, Object>) - Static method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl: This is basically stolen from org.galaxyproject.gxformat2.Lint.
isList() - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
isOne() - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf

L

Labeled - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/cwl#Labeled
Labeled - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
launchInstructions(String) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
lint(String[]) - Static method in class org.galaxyproject.gxformat2.Lint
lint(Map<String, Object>) - Static method in class org.galaxyproject.gxformat2.Lint
lint(LintContext, Map<String, Object>) - Method in class org.galaxyproject.gxformat2.Format2Linter
lint(LintContext, Map<String, Object>) - Method in interface org.galaxyproject.gxformat2.GalaxyWorkflowLinter
lint(LintContext, Map<String, Object>) - Method in class org.galaxyproject.gxformat2.NativeLinter
Lint - Class in org.galaxyproject.gxformat2
Lint() - Constructor for class org.galaxyproject.gxformat2.Lint
LINT_FAILED_NO_OUTPUTS - Static variable in class org.galaxyproject.gxformat2.NativeLinter
LINT_FAILED_OUTPUT_NO_LABEL - Static variable in class org.galaxyproject.gxformat2.NativeLinter
LintContext - Class in org.galaxyproject.gxformat2
listOf(List<T>) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
load(Object, String, LoadingOptions) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.AnyLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.ArrayLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.EnumLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.IdMapLoader
load(Object, String, LoadingOptions, String) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.NullLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOfLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.OptionalLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.PrimitiveLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.RecordLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.TypeDslLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.UnionLoader
load(Object, String, LoadingOptions, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.UriLoader
loadCytoscapeElements(String, String, Map<String, MinimalLanguageInterface.FileMetadata>) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
loadDocument(File) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(File, String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(File, String, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(File, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(String, String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(String, String, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(String, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Path) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Path, String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Path, String, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Path, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Map<String, Object>) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Map<String, Object>, String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
loadDocument(Map<String, Object>, String, LoadingOptions) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
Loader<T> - Interface in org.galaxyproject.gxformat2.v19_09.utils
LoaderInstances - Class in org.galaxyproject.gxformat2.v19_09.utils
LoaderInstances() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
loadField(Object, String, LoadingOptions) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
LoadingOptions - Class in org.galaxyproject.gxformat2.v19_09.utils
LoadingOptionsBuilder - Class in org.galaxyproject.gxformat2.v19_09.utils
LoadingOptionsBuilder() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder
LOG - Static variable in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin
LONG - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
LongInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances

M

main(String[]) - Static method in class org.galaxyproject.gxformat2.Lint
main(String[]) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Validator
MAIN_TS_PREFIX - Static variable in class org.galaxyproject.gxformat2.Cytoscape
mapFromString(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.YamlUtils

N

NativeLinter - Class in org.galaxyproject.gxformat2
NativeLinter() - Constructor for class org.galaxyproject.gxformat2.NativeLinter
NativeWorkflowAdapter - Class in org.galaxyproject.gxformat2
NativeWorkflowAdapter(Map<String, Object>) - Constructor for class org.galaxyproject.gxformat2.NativeWorkflowAdapter
Node() - Constructor for class org.galaxyproject.gxformat2.CytoscapeDAG.Node
NodeData() - Constructor for class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
NormalizedStep() - Constructor for class org.galaxyproject.gxformat2.WorkflowAdapter.NormalizedStep
normalizedSteps() - Method in class org.galaxyproject.gxformat2.Format2WorkflowAdapter
normalizedSteps() - Method in class org.galaxyproject.gxformat2.NativeWorkflowAdapter
normalizedSteps() - Method in interface org.galaxyproject.gxformat2.WorkflowAdapter
NULL - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
NullInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
NullLoader - Class in org.galaxyproject.gxformat2.v19_09.utils
NullLoader() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.NullLoader

O

objectMapper - Static variable in class org.galaxyproject.gxformat2.Cytoscape
oneOf(T) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOf
OneOrListOf<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
OneOrListOfLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
OneOrListOfLoader(Loader<T>, Loader<List<T>>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.OneOrListOfLoader
optional_AnyInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_array_of_RecordField - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_array_of_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_array_of_union_of_StringInstance_or_WorkflowStepOutput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_array_of_WorkflowStepInput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_BooleanInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_GalaxyType - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_GalaxyWorkflow - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_Report - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_StepPosition - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_ToolShedRepository - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
optional_WorkflowStepType - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
OptionalLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
OptionalLoader(Loader<T>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.OptionalLoader
org.galaxyproject.dockstore_galaxy_interface.language - package org.galaxyproject.dockstore_galaxy_interface.language
org.galaxyproject.gxformat2 - package org.galaxyproject.gxformat2
org.galaxyproject.gxformat2.v19_09 - package org.galaxyproject.gxformat2.v19_09: Package for the auto-generated Java objects corresponding generated by Schema Salad for https://galaxyproject.org/gxformat2/v19_09#.
org.galaxyproject.gxformat2.v19_09.utils - package org.galaxyproject.gxformat2.v19_09.utils: This package contains utilities for working the SchemaSalad generated code for the org.galaxyproject.gxformat2.v19_09 package.
OutputParameter - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter
OutputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances

P

Parameter - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/cwl#Parameter
Define an input or output parameter to a process.
Parameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
parseWorkflowForMetadata(String, String, Map<String, MinimalLanguageInterface.FileMetadata>) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
pathExistsFromReader(MinimalLanguageInterface.FileReader, String) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
PAUSE - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.WorkflowStepType
prettyStr(Integer) - Method in exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
PrimitiveLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
PrimitiveLoader(Class<T>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.PrimitiveLoader
PrimitiveType - Enum Class in org.galaxyproject.gxformat2.v19_09
PrimitiveType - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
printMessages() - Method in class org.galaxyproject.gxformat2.LintContext
Process - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/cwl#Process
The base executable type in CWL is the `Process` object defined by the document.
Process - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances

Q

quote(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris

R

readYamlFromPath(String) - Static method in class org.galaxyproject.gxformat2.IoUtils
readYamlFromPath(Path) - Static method in class org.galaxyproject.gxformat2.IoUtils
RECORD - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.enum_d9cba076fca539106791a4f46d198c7fcfbdb779
RecordField - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/salad#RecordField
This interface is implemented by RecordFieldImpl
A field of a record.
RecordField - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
RecordFieldImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://w3id.org/cwl/salad#RecordField
A field of a record.
RecordFieldImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.RecordFieldImpl: Used by RootLoader to construct instances of RecordFieldImpl.
RecordLoader<T extends Savable> - Class in org.galaxyproject.gxformat2.v19_09.utils
RecordLoader(Class<? extends T>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.RecordLoader
RecordSchema - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema
This interface is implemented by RecordSchemaImpl
RecordSchema - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
RecordSchemaImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://w3id.org/cwl/salad#RecordSchema
RecordSchemaImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.RecordSchemaImpl: Used by RootLoader to construct instances of RecordSchemaImpl.
ReferencesTool - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool
ReferencesTool - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
Report - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#Report
This interface is implemented by ReportImpl
Definition of an invocation report for this workflow.
Report - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
ReportImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#Report
Definition of an invocation report for this workflow.
ReportImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.ReportImpl: Used by RootLoader to construct instances of ReportImpl.
RootLoader - Class in org.galaxyproject.gxformat2.v19_09.utils
RootLoader() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.RootLoader
rvocab - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.ConstantMaps

S

Savable - Interface in org.galaxyproject.gxformat2.v19_09.utils
SavableImpl - Class in org.galaxyproject.gxformat2.v19_09.utils
SavableImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.SavableImpl
setData(CytoscapeDAG.Edge.EdgeData) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge
setData(CytoscapeDAG.Node.NodeData) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node
setDocker(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
setEdges(List<CytoscapeDAG.Edge>) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG
setFetcher(Fetcher) - Method in class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder
setFileUri(String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder
setId(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
setId(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
setName(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
setNamespaces(Map<String, String>) - Method in class org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder
setNodes(List<CytoscapeDAG.Node>) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG
setRun(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Node.NodeData
setSource(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
setTarget(String) - Method in class org.galaxyproject.gxformat2.CytoscapeDAG.Edge.EdgeData
simplify() - Method in exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
Sink - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#Sink
Sink - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
split(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris
START_ID - Static variable in class org.galaxyproject.gxformat2.Cytoscape
StepPosition - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#StepPosition
This interface is implemented by StepPositionImpl
This field specifies the location of the step's node when rendered in the workflow editor.
StepPosition - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
StepPositionImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/gxformat2common#StepPosition
This field specifies the location of the step's node when rendered in the workflow editor.
StepPositionImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.StepPositionImpl: Used by RootLoader to construct instances of StepPositionImpl.
STRING - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType
StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
SUBWORKFLOW - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.WorkflowStepType
summary(int, boolean) - Method in exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException

T

TEST_EXTENSIONS - Static variable in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin
TEST_SUFFIXES - Static variable in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin
TEXT - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType
TOOL - Enum constant in enum class org.galaxyproject.gxformat2.v19_09.WorkflowStepType
ToolShedRepository - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository
This interface is implemented by ToolShedRepositoryImpl
ToolShedRepository - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
ToolShedRepositoryImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository
ToolShedRepositoryImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.ToolShedRepositoryImpl: Used by RootLoader to construct instances of ToolShedRepositoryImpl.
toString() - Method in class org.galaxyproject.gxformat2.v19_09.utils.Uris.UriSplit
toUri(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris
typedsl_enum_d062602be0b4b8fd33e69e29a841317b6ab665bc_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
typedsl_enum_d961d79c225752b9fadb617367615ab176b47d77_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
typedsl_enum_d9cba076fca539106791a4f46d198c7fcfbdb779_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
typedsl_optional_GalaxyType_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
typedsl_optional_WorkflowStepType_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
typedsl_union_of_GalaxyType_or_StringInstance_or_NullInstance_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
TypeDslLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
TypeDslLoader(Loader<T>, Integer) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.TypeDslLoader

U

union_of_FloatInstance_or_IntegerInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
union_of_GalaxyType_or_StringInstance_or_NullInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
union_of_GalaxyWorkflow_or_array_of_GalaxyWorkflow - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
union_of_StringInstance_or_WorkflowStepOutput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
UnionLoader - Class in org.galaxyproject.gxformat2.v19_09.utils
UnionLoader(List<Loader>) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.UnionLoader
UnionLoader(Loader[]) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.UnionLoader
unquote(String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris
unsplit(String, String, String, String, String) - Static method in class org.galaxyproject.gxformat2.v19_09.utils.Uris
uri_array_of_StringInstance_True_False_None - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
uri_optional_GalaxyWorkflow_False_False_None - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
uri_optional_StringInstance_True_False_None - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
uri_StringInstance_False_True_None - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
uri_StringInstance_True_False_None - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_StringInstance_False_True_2 - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
UriLoader<T> - Class in org.galaxyproject.gxformat2.v19_09.utils
UriLoader(Loader<T>, boolean, boolean, Integer) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.UriLoader
Uris - Class in org.galaxyproject.gxformat2.v19_09.utils
Uris() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.Uris
Uris.UriSplit - Class in org.galaxyproject.gxformat2.v19_09.utils
UriSplit(String, String, String, String, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.Uris.UriSplit
urlJoin(String, String) - Method in class org.galaxyproject.gxformat2.v19_09.utils.DefaultFetcher
urlJoin(String, String) - Method in interface org.galaxyproject.gxformat2.v19_09.utils.Fetcher

V

validateOfJavaType(Class<T>, Object) - Static method in interface org.galaxyproject.gxformat2.v19_09.utils.Loader
validateTestParameterSet(Map<String, MinimalLanguageInterface.FileMetadata>) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
validateWorkflowSet(String, String, Map<String, MinimalLanguageInterface.FileMetadata>) - Method in class org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
ValidationException - Exception in org.galaxyproject.gxformat2.v19_09.utils
ValidationException(String) - Constructor for exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
ValidationException(String, List<ValidationException>) - Constructor for exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
ValidationException(String, ValidationException) - Constructor for exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
Validator - Class in org.galaxyproject.gxformat2.v19_09.utils
Validator() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.Validator
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.Any: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d062602be0b4b8fd33e69e29a841317b6ab665bc: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d961d79c225752b9fadb617367615ab176b47d77: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d9cba076fca539106791a4f46d198c7fcfbdb779: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.galaxyproject.gxformat2.v19_09.WorkflowStepType: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.Any: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d062602be0b4b8fd33e69e29a841317b6ab665bc: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d961d79c225752b9fadb617367615ab176b47d77: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.enum_d9cba076fca539106791a4f46d198c7fcfbdb779: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.GalaxyType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.PrimitiveType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.galaxyproject.gxformat2.v19_09.WorkflowStepType: Returns an array containing the constants of this enum class, in the order they are declared.
vocab - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.ConstantMaps

W

withBullet(String) - Method in exception org.galaxyproject.gxformat2.v19_09.utils.ValidationException
WorkflowAdapter - Interface in org.galaxyproject.gxformat2
WorkflowAdapter.Input - Class in org.galaxyproject.gxformat2
WorkflowAdapter.NormalizedStep - Class in org.galaxyproject.gxformat2
WorkflowInputParameter - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter
This interface is implemented by WorkflowInputParameterImpl
WorkflowInputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
WorkflowInputParameterImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter
WorkflowInputParameterImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.WorkflowInputParameterImpl: Used by RootLoader to construct instances of WorkflowInputParameterImpl.
WorkflowOutputParameter - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter
This interface is implemented by WorkflowOutputParameterImpl
Describe an output parameter of a workflow.
WorkflowOutputParameter - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
WorkflowOutputParameterImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter
Describe an output parameter of a workflow.
WorkflowOutputParameterImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.WorkflowOutputParameterImpl: Used by RootLoader to construct instances of WorkflowOutputParameterImpl.
WorkflowStep - Interface in org.galaxyproject.gxformat2.v19_09: 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.
WorkflowStep - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
WorkflowStepImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowStep
This represents a non-input step a Galaxy Workflow.
WorkflowStepImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl: Used by RootLoader to construct instances of WorkflowStepImpl.
WorkflowStepInput - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput
This interface is implemented by WorkflowStepInputImpl
TODO:
WorkflowStepInput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
WorkflowStepInputImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput
TODO:
WorkflowStepInputImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.WorkflowStepInputImpl: Used by RootLoader to construct instances of WorkflowStepInputImpl.
WorkflowStepOutput - Interface in org.galaxyproject.gxformat2.v19_09: Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput
This interface is implemented by WorkflowStepOutputImpl
Associate an output parameter of the underlying process with a workflow parameter.
WorkflowStepOutput - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances
WorkflowStepOutputImpl - Class in org.galaxyproject.gxformat2.v19_09: Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput
Associate an output parameter of the underlying process with a workflow parameter.
WorkflowStepOutputImpl(Object, String, LoadingOptions, String) - Constructor for class org.galaxyproject.gxformat2.v19_09.WorkflowStepOutputImpl: Used by RootLoader to construct instances of WorkflowStepOutputImpl.
WorkflowStepType - Enum Class in org.galaxyproject.gxformat2.v19_09
WorkflowStepType - Static variable in class org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances

Y

YamlUtils - Class in org.galaxyproject.gxformat2.v19_09.utils
YamlUtils() - Constructor for class org.galaxyproject.gxformat2.v19_09.utils.YamlUtils

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