Index

A

a_galaxy_workflow (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) action_arguments (gxformat2.schema.native.NativePostJobAction attribute) (gxformat2.schema.native_strict.NativePostJobAction attribute) action_type (gxformat2.schema.native.NativePostJobAction attribute) (gxformat2.schema.native_strict.NativePostJobAction attribute) add_tags (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) addl_metadata (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) address (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) ALL (gxformat2.linting.LintLevel attribute) alternateName (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) annotation (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeStep attribute) AnyLoader (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) applies_to (gxformat2.lint_rules.NativeStepKeyNotInteger attribute) (gxformat2.linting.Linter attribute) (gxformat2.schema_rules.SchemaRule attribute) AppliesTo (class in gxformat2.schema_rules) ArraySchema (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) assert_value() (in module gxformat2.testing) assert_value_any_contains() (in module gxformat2.testing) assert_value_contains() (in module gxformat2.testing) assert_value_falsy() (in module gxformat2.testing) assert_value_matches() (in module gxformat2.testing) assert_value_set() (in module gxformat2.testing) assert_value_truthy() (in module gxformat2.testing) assert_value_type() (in module gxformat2.testing) Assertion (class in gxformat2.testing) assertions (gxformat2.testing.TestCase attribute) attrs (gxformat2.schema.native_v0_1.ArraySchema attribute) (gxformat2.schema.native_v0_1.EnumSchema attribute) (gxformat2.schema.native_v0_1.NativeCreatorOrganization attribute) (gxformat2.schema.native_v0_1.NativeCreatorPerson attribute) (gxformat2.schema.native_v0_1.NativeFrameComment attribute) (gxformat2.schema.native_v0_1.NativeFrameCommentData attribute) (gxformat2.schema.native_v0_1.NativeFreehandComment attribute) (gxformat2.schema.native_v0_1.NativeFreehandCommentData attribute) (gxformat2.schema.native_v0_1.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_v0_1.NativeInputConnection attribute) (gxformat2.schema.native_v0_1.NativeMarkdownComment attribute) (gxformat2.schema.native_v0_1.NativeMarkdownCommentData attribute) (gxformat2.schema.native_v0_1.NativePostJobAction attribute) (gxformat2.schema.native_v0_1.NativeReport attribute) (gxformat2.schema.native_v0_1.NativeSourceMetadata attribute) (gxformat2.schema.native_v0_1.NativeStep attribute) (gxformat2.schema.native_v0_1.NativeStepInput attribute) (gxformat2.schema.native_v0_1.NativeStepOutput attribute) (gxformat2.schema.native_v0_1.NativeTextComment attribute) (gxformat2.schema.native_v0_1.NativeTextCommentData attribute) (gxformat2.schema.native_v0_1.NativeWorkflowOutput attribute) (gxformat2.schema.native_v0_1.RecordField attribute) (gxformat2.schema.native_v0_1.RecordFieldDefinition attribute) (gxformat2.schema.native_v0_1.RecordSchema attribute) (gxformat2.schema.native_v0_1.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_v0_1.StepPosition attribute) (gxformat2.schema.native_v0_1.ToolShedRepository attribute) (gxformat2.schema.native_v0_1.WorkflowTextOption attribute) (gxformat2.schema.v19_09.ArraySchema attribute) (gxformat2.schema.v19_09.BaseDataParameter attribute) (gxformat2.schema.v19_09.BaseInputParameter attribute) (gxformat2.schema.v19_09.CreatorOrganization attribute) (gxformat2.schema.v19_09.CreatorPerson attribute) (gxformat2.schema.v19_09.EnumSchema attribute) (gxformat2.schema.v19_09.FrameComment attribute) (gxformat2.schema.v19_09.FreehandComment attribute) (gxformat2.schema.v19_09.GalaxyWorkflow attribute) (gxformat2.schema.v19_09.MarkdownComment attribute) (gxformat2.schema.v19_09.MinMax attribute) (gxformat2.schema.v19_09.RecordField attribute) (gxformat2.schema.v19_09.RecordFieldDefinition attribute) (gxformat2.schema.v19_09.RecordSchema attribute) (gxformat2.schema.v19_09.Report attribute) (gxformat2.schema.v19_09.SampleSheetColumnDefinition attribute) (gxformat2.schema.v19_09.StepPosition attribute) (gxformat2.schema.v19_09.TextComment attribute) (gxformat2.schema.v19_09.ToolShedRepository attribute) (gxformat2.schema.v19_09.WorkflowBooleanParameter attribute) (gxformat2.schema.v19_09.WorkflowCollectionParameter attribute) (gxformat2.schema.v19_09.WorkflowDataParameter attribute) (gxformat2.schema.v19_09.WorkflowFloatParameter attribute) (gxformat2.schema.v19_09.WorkflowInputParameter attribute) (gxformat2.schema.v19_09.WorkflowIntegerParameter attribute) (gxformat2.schema.v19_09.WorkflowOutputParameter attribute) (gxformat2.schema.v19_09.WorkflowStep attribute) (gxformat2.schema.v19_09.WorkflowStepInput attribute) (gxformat2.schema.v19_09.WorkflowStepOutput attribute) (gxformat2.schema.v19_09.WorkflowTextOption attribute) (gxformat2.schema.v19_09.WorkflowTextParameter attribute)

B

bakes_coordinates() (in module gxformat2.cytoscape) BaseComment (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) BaseCreator (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) BaseDataParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) BaseInputParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) BaseNativeComment (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1)

BaseNativeCreator (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) baseuri (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) BioBlendImporterGalaxyInterface (class in gxformat2.interface) bold (gxformat2.schema.gxformat2.TextComment attribute) (gxformat2.schema.gxformat2_strict.TextComment attribute) (gxformat2.schema.native.NativeTextCommentData attribute) (gxformat2.schema.native_strict.NativeTextCommentData attribute) boolean (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute) both (gxformat2.schema_rules.Scope attribute)

C

cache (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) cases (gxformat2.testing.DeclarativeTestSuite property) CatalogEntry (class in gxformat2.examples) change_datatype (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) changeset_revision (gxformat2.schema.gxformat2.ToolShedRepository attribute) (gxformat2.schema.gxformat2_strict.ToolShedRepository attribute) (gxformat2.schema.native.ToolShedRepository attribute) (gxformat2.schema.native_strict.ToolShedRepository attribute) child() (gxformat2.linting.LintContext method) child_comments (gxformat2.schema.native.NativeFrameComment attribute) (gxformat2.schema.native_strict.NativeFrameComment attribute) child_steps (gxformat2.schema.native.NativeFrameComment attribute) (gxformat2.schema.native_strict.NativeFrameComment attribute) class_ (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.schema.gxformat2.CreatorOrganization attribute) (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.CreatorOrganization attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeCreatorOrganization attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeCreatorOrganization attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) (gxformat2.schema.v19_09.CreatorOrganization attribute) (gxformat2.schema.v19_09.CreatorPerson attribute) (gxformat2.schema.v19_09.GalaxyWorkflow attribute) classes (gxformat2.cytoscape.CytoscapeNode attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) collection (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) collection_type (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) color (gxformat2.schema.gxformat2.BaseComment attribute) (gxformat2.schema.gxformat2_strict.BaseComment attribute) (gxformat2.schema.native.BaseNativeComment attribute) (gxformat2.schema.native_strict.BaseNativeComment attribute) column_definitions (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) comments (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute)

connected_paths (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) container (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) contains_comments (gxformat2.schema.gxformat2.FrameComment attribute) (gxformat2.schema.gxformat2_strict.FrameComment attribute) contains_steps (gxformat2.schema.gxformat2.FrameComment attribute) (gxformat2.schema.gxformat2_strict.FrameComment attribute) content_id (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) content_source (gxformat2.normalized.NormalizedNativeStep attribute) ConversionOptions (class in gxformat2) (class in gxformat2.options) convert_typing() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) converted (gxformat2.examples.ExampleOrigin attribute) creator (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) CreatorOrganization (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) CreatorOrganizationTypeLoader (in module gxformat2.schema.v19_09) CreatorPerson (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) CreatorPersonTypeLoader (in module gxformat2.schema.v19_09) cytoscape_elements() (in module gxformat2.cytoscape) CytoscapeEdge (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models) CytoscapeEdgeData (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models) CytoscapeElements (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models) CytoscapeLayout (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models) CytoscapeNode (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models) CytoscapeNodeData (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models) CytoscapePosition (class in gxformat2.cytoscape) (class in gxformat2.cytoscape.models)

D

data (gxformat2.cytoscape.CytoscapeEdge attribute) (gxformat2.cytoscape.CytoscapeNode attribute) (gxformat2.cytoscape.models.CytoscapeEdge attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.native.NativeFrameComment attribute) (gxformat2.schema.native.NativeFreehandComment attribute) (gxformat2.schema.native.NativeMarkdownComment attribute) (gxformat2.schema.native.NativeTextComment attribute) (gxformat2.schema.native_strict.NativeFrameComment attribute) (gxformat2.schema.native_strict.NativeFreehandComment attribute) (gxformat2.schema.native_strict.NativeMarkdownComment attribute) (gxformat2.schema.native_strict.NativeTextComment attribute) data_collection_input (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStepType attribute) data_input (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStepType attribute) DeclarativeTestSuite (class in gxformat2.testing) default (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.InputParameter attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowStepInput attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.InputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepInput attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) default_url_resolver() (in module gxformat2.options) default_value (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) delete_intermediate_datasets (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) description (gxformat2.lint_profiles.LintProfile attribute) (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.native.NativeStepInput attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.NativeStepInput attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema_rules.SchemaRule attribute)

doc (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.BaseInputParameter attribute) (gxformat2.schema.gxformat2.Documented attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2.InputParameter attribute) (gxformat2.schema.gxformat2.OutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.BaseInputParameter attribute) (gxformat2.schema.gxformat2_strict.Documented attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.InputParameter attribute) (gxformat2.schema.gxformat2_strict.OutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.Documented attribute) (gxformat2.schema.native_strict.Documented attribute) Documented (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) doi (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) double (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute)

E

edges (gxformat2.cytoscape.CytoscapeElements attribute) (gxformat2.cytoscape.models.CytoscapeElements attribute) email (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) ensure_format2() (in module gxformat2.normalized) ensure_native() (in module gxformat2.normalized) ensure_step_position() (in module gxformat2.model) EnumSchema (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) ERROR (gxformat2.linting.LintLevel attribute) error (gxformat2.schema_rules.Severity attribute) error() (gxformat2.linting.LintContext method) error_messages (gxformat2.linting.LintContext attribute)

errors (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.HasStepErrors attribute) (gxformat2.schema.gxformat2_strict.HasStepErrors attribute) (gxformat2.schema.native.HasStepErrors attribute) (gxformat2.schema.native_strict.HasStepErrors attribute) ExampleFormat (class in gxformat2.examples) ExampleOrigin (class in gxformat2.examples) expand_url() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) expanded_format2() (in module gxformat2.normalized) expanded_native() (in module gxformat2.normalized) ExpandedFormat2 (class in gxformat2.normalized) ExpandedNativeStep (class in gxformat2.normalized) ExpandedNativeWorkflow (class in gxformat2.normalized) ExpandedWorkflowStep (class in gxformat2.normalized) expect_error (gxformat2.testing.TestCase attribute) ExpectationSuite (class in gxformat2.testing) extract_type() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09)

F

familyName (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute) faxNumber (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) fetcher (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) fields (gxformat2.schema.gxformat2.RecordSchema attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.RecordSchema attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.native.RecordSchema attribute) (gxformat2.schema.native_strict.RecordSchema attribute) file (gxformat2.examples.CatalogEntry attribute) File (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) file_uri() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) fileuri (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) fixture (gxformat2.testing.TestCase attribute) float (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute) format (gxformat2.examples.CatalogEntry attribute) (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.RecordFieldDefinition attribute) (gxformat2.schema.native.RecordFieldDefinition attribute) (gxformat2.schema.native_strict.RecordFieldDefinition attribute) format2 (gxformat2.examples.ExampleFormat attribute) (gxformat2.schema_rules.AppliesTo attribute) format_version (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) FrameComment (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) FreehandComment (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) from_dict() (in module gxformat2.abstract) from_galaxy_native() (in module gxformat2) (in module gxformat2.export) from_yaml() (gxformat2.testing.ExpectationSuite class method) fromDoc() (gxformat2.schema.native_v0_1.ArraySchema class method) (gxformat2.schema.native_v0_1.EnumSchema class method) (gxformat2.schema.native_v0_1.NativeCreatorOrganization class method) (gxformat2.schema.native_v0_1.NativeCreatorPerson class method) (gxformat2.schema.native_v0_1.NativeFrameComment class method) (gxformat2.schema.native_v0_1.NativeFrameCommentData class method) (gxformat2.schema.native_v0_1.NativeFreehandComment class method) (gxformat2.schema.native_v0_1.NativeFreehandCommentData class method) (gxformat2.schema.native_v0_1.NativeGalaxyWorkflow class method) (gxformat2.schema.native_v0_1.NativeInputConnection class method) (gxformat2.schema.native_v0_1.NativeMarkdownComment class method) (gxformat2.schema.native_v0_1.NativeMarkdownCommentData class method) (gxformat2.schema.native_v0_1.NativePostJobAction class method) (gxformat2.schema.native_v0_1.NativeReport class method) (gxformat2.schema.native_v0_1.NativeSourceMetadata class method) (gxformat2.schema.native_v0_1.NativeStep class method) (gxformat2.schema.native_v0_1.NativeStepInput class method) (gxformat2.schema.native_v0_1.NativeStepOutput class method) (gxformat2.schema.native_v0_1.NativeTextComment class method) (gxformat2.schema.native_v0_1.NativeTextCommentData class method) (gxformat2.schema.native_v0_1.NativeWorkflowOutput class method) (gxformat2.schema.native_v0_1.RecordField class method) (gxformat2.schema.native_v0_1.RecordFieldDefinition class method) (gxformat2.schema.native_v0_1.RecordSchema class method) (gxformat2.schema.native_v0_1.SampleSheetColumnDefinition class method) (gxformat2.schema.native_v0_1.Saveable class method) (gxformat2.schema.native_v0_1.StepPosition class method) (gxformat2.schema.native_v0_1.ToolShedRepository class method) (gxformat2.schema.native_v0_1.WorkflowTextOption class method) (gxformat2.schema.v19_09.ArraySchema class method) (gxformat2.schema.v19_09.BaseDataParameter class method) (gxformat2.schema.v19_09.BaseInputParameter class method) (gxformat2.schema.v19_09.CreatorOrganization class method) (gxformat2.schema.v19_09.CreatorPerson class method) (gxformat2.schema.v19_09.EnumSchema class method) (gxformat2.schema.v19_09.FrameComment class method) (gxformat2.schema.v19_09.FreehandComment class method) (gxformat2.schema.v19_09.GalaxyWorkflow class method) (gxformat2.schema.v19_09.MarkdownComment class method) (gxformat2.schema.v19_09.MinMax class method) (gxformat2.schema.v19_09.RecordField class method) (gxformat2.schema.v19_09.RecordFieldDefinition class method) (gxformat2.schema.v19_09.RecordSchema class method) (gxformat2.schema.v19_09.Report class method) (gxformat2.schema.v19_09.SampleSheetColumnDefinition class method) (gxformat2.schema.v19_09.Saveable class method) (gxformat2.schema.v19_09.StepPosition class method) (gxformat2.schema.v19_09.TextComment class method) (gxformat2.schema.v19_09.ToolShedRepository class method) (gxformat2.schema.v19_09.WorkflowBooleanParameter class method) (gxformat2.schema.v19_09.WorkflowCollectionParameter class method) (gxformat2.schema.v19_09.WorkflowDataParameter class method) (gxformat2.schema.v19_09.WorkflowFloatParameter class method) (gxformat2.schema.v19_09.WorkflowInputParameter class method) (gxformat2.schema.v19_09.WorkflowIntegerParameter class method) (gxformat2.schema.v19_09.WorkflowOutputParameter class method) (gxformat2.schema.v19_09.WorkflowStep class method) (gxformat2.schema.v19_09.WorkflowStepInput class method) (gxformat2.schema.v19_09.WorkflowStepOutput class method) (gxformat2.schema.v19_09.WorkflowTextOption class method) (gxformat2.schema.v19_09.WorkflowTextParameter class method)

G

GalaxyType (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) GalaxyTypeLoader (in module gxformat2.schema.v19_09) GalaxyWorkflow (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) generate() (gxformat2.schema.json_schema.GxFormat2GenerateJsonSchema method) get_native_step_type() (in module gxformat2.model) get_path() (in module gxformat2.examples) givenName (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute) graph (gxformat2.schema.native_v0_1.LoadingOptions property) (gxformat2.schema.v19_09.LoadingOptions property) group (gxformat2.cytoscape.CytoscapeEdge attribute) (gxformat2.cytoscape.CytoscapeNode attribute) (gxformat2.cytoscape.models.CytoscapeEdge attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) gxformat2 module gxformat2.abstract module gxformat2.converter module gxformat2.cytoscape module gxformat2.cytoscape.models module gxformat2.examples module gxformat2.export module gxformat2.interface module gxformat2.lint module gxformat2.lint_profiles module gxformat2.lint_rules module

gxformat2.linting module gxformat2.markdown_parse module gxformat2.mermaid module gxformat2.model module gxformat2.normalize module gxformat2.normalized module gxformat2.options module gxformat2.schema module gxformat2.schema.gxformat2 module gxformat2.schema.gxformat2_strict module gxformat2.schema.json_schema module gxformat2.schema.native module gxformat2.schema.native_strict module gxformat2.schema.native_v0_1 module gxformat2.schema.v19_09 module gxformat2.schema_rules module gxformat2.testing module gxformat2.validators module gxformat2.yaml module GxFormat2GenerateJsonSchema (class in gxformat2.schema.json_schema)

H

HasStepErrors (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) HasStepPosition (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) HasUUID (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09)

help (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) hide (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) honorificPrefix (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute) honorificSuffix (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute)

I

id (gxformat2.cytoscape.CytoscapeEdgeData attribute) (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.lint_profiles.LintProfile attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.BaseInputParameter attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2.Identified attribute) (gxformat2.schema.gxformat2.InputParameter attribute) (gxformat2.schema.gxformat2.OutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.BaseInputParameter attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.Identified attribute) (gxformat2.schema.gxformat2_strict.InputParameter attribute) (gxformat2.schema.gxformat2_strict.OutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.BaseNativeComment attribute) (gxformat2.schema.native.NativeInputConnection attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.BaseNativeComment attribute) (gxformat2.schema.native_strict.NativeInputConnection attribute) (gxformat2.schema.native_strict.NativeStep attribute) (gxformat2.schema.v19_09.BaseDataParameter attribute) (gxformat2.schema.v19_09.BaseInputParameter attribute) (gxformat2.schema.v19_09.GalaxyWorkflow attribute) (gxformat2.schema.v19_09.WorkflowBooleanParameter attribute) (gxformat2.schema.v19_09.WorkflowCollectionParameter attribute) (gxformat2.schema.v19_09.WorkflowDataParameter attribute) (gxformat2.schema.v19_09.WorkflowFloatParameter attribute) (gxformat2.schema.v19_09.WorkflowInputParameter attribute) (gxformat2.schema.v19_09.WorkflowIntegerParameter attribute) (gxformat2.schema.v19_09.WorkflowOutputParameter attribute) (gxformat2.schema.v19_09.WorkflowStep attribute) (gxformat2.schema.v19_09.WorkflowStepInput attribute) (gxformat2.schema.v19_09.WorkflowStepOutput attribute) (gxformat2.schema.v19_09.WorkflowTextParameter attribute) (gxformat2.schema_rules.SchemaRule attribute) Identified (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) identifier (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) idx (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) image (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute)

import_workflow() (gxformat2.interface.BioBlendImporterGalaxyInterface method) (gxformat2.interface.ImporterGalaxyInterface method) ImporterGalaxyInterface (class in gxformat2.interface) ImportOptions (class in gxformat2) imports (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) in_ (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) includes (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) inline_tool_class (gxformat2.normalized.NormalizedNativeStep property) inline_tool_representation (gxformat2.normalized.NormalizedWorkflowStep property) input (gxformat2.cytoscape.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) input_connections (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) input_parameter_class() (in module gxformat2.schema.gxformat2) (in module gxformat2.schema.gxformat2_strict) input_subworkflow_step_id (gxformat2.schema.native.NativeInputConnection attribute) (gxformat2.schema.native_strict.NativeInputConnection attribute) InputParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) inputs (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.gxformat2.Process attribute) (gxformat2.schema.gxformat2_strict.Process attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) inputs() (in module gxformat2.normalize) inputs_normalized() (in module gxformat2.normalize) int (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute) integer (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) is_inline_tool_step (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_input_step (gxformat2.normalized.NormalizedNativeStep property) is_layout_name() (in module gxformat2.cytoscape) is_pause_step (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_pick_value_step (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_subworkflow_step (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_tool_step (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_trs_url() (in module gxformat2.options) italic (gxformat2.schema.gxformat2.TextComment attribute) (gxformat2.schema.gxformat2_strict.TextComment attribute) (gxformat2.schema.native.NativeTextCommentData attribute) (gxformat2.schema.native_strict.NativeTextCommentData attribute) items (gxformat2.schema.gxformat2.ArraySchema attribute) (gxformat2.schema.gxformat2_strict.ArraySchema attribute) (gxformat2.schema.native.ArraySchema attribute) (gxformat2.schema.native_strict.ArraySchema attribute) iwc_rule_ids() (in module gxformat2.lint_profiles)

J

jobTitle (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute)

json_pointer (gxformat2.linting.LintMessage attribute)

K

known_labels (gxformat2.normalized.NormalizedFormat2 property)

L

label (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.BaseComment attribute) (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.BaseInputParameter attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2.InputParameter attribute) (gxformat2.schema.gxformat2.Labeled attribute) (gxformat2.schema.gxformat2.OutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextOption attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.BaseComment attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.BaseInputParameter attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.InputParameter attribute) (gxformat2.schema.gxformat2_strict.Labeled attribute) (gxformat2.schema.gxformat2_strict.OutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextOption attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native.NativeWorkflowOutput attribute) (gxformat2.schema.native.WorkflowTextOption attribute) (gxformat2.schema.native_strict.NativeStep attribute) (gxformat2.schema.native_strict.NativeWorkflowOutput attribute) (gxformat2.schema.native_strict.WorkflowTextOption attribute) Labeled (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) lax (gxformat2.schema_rules.Scope attribute) layout (gxformat2.cytoscape.CytoscapeElements attribute) (gxformat2.cytoscape.models.CytoscapeElements attribute) left (gxformat2.schema.gxformat2.StepPosition attribute) (gxformat2.schema.gxformat2_strict.StepPosition attribute) (gxformat2.schema.native.StepPosition attribute) (gxformat2.schema.native_strict.StepPosition attribute) level (gxformat2.linting.LintMessage attribute) license (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute)

line (gxformat2.schema.gxformat2.FreehandComment attribute) (gxformat2.schema.gxformat2_strict.FreehandComment attribute) (gxformat2.schema.native.NativeFreehandCommentData attribute) (gxformat2.schema.native_strict.NativeFreehandCommentData attribute) lint_best_practices() (in module gxformat2.lint) lint_best_practices_format2() (in module gxformat2.lint) lint_best_practices_ga() (in module gxformat2.lint) lint_format2() (in module gxformat2.lint) lint_ga() (in module gxformat2.lint) lint_profiles_by_id() (in module gxformat2.lint_profiles) lint_pydantic_validation() (in module gxformat2.lint) LintContext (class in gxformat2.linting) Linter (class in gxformat2.linting) linter (gxformat2.linting.LintMessage attribute) LintLevel (class in gxformat2.linting) LintMessage (class in gxformat2.linting) LintProfile (class in gxformat2.lint_profiles) load() (gxformat2.examples.CatalogEntry method) (in module gxformat2.examples) load_catalog() (in module gxformat2.examples) load_contents() (gxformat2.examples.CatalogEntry method) (in module gxformat2.examples) load_document() (in module gxformat2.schema.gxformat2) (in module gxformat2.schema.gxformat2_strict) (in module gxformat2.schema.native) (in module gxformat2.schema.native_strict) (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) load_document_by_string() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) load_document_by_yaml() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) load_document_with_metadata() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) load_expectation_cases() (in module gxformat2.testing) load_field() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) load_lint_profiles() (in module gxformat2.lint_profiles) load_schema_rules() (in module gxformat2.schema_rules) LoadingOptions (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) logo_url (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) long (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute)

M

main() (in module gxformat2.abstract) (in module gxformat2.converter) (in module gxformat2.cytoscape) (in module gxformat2.export) (in module gxformat2.lint) (in module gxformat2.mermaid) markdown (gxformat2.schema.gxformat2.Report attribute) (gxformat2.schema.gxformat2_strict.Report attribute) (gxformat2.schema.native.NativeReport attribute) (gxformat2.schema.native_strict.NativeReport attribute) MarkdownComment (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) max (gxformat2.schema.gxformat2.MinMax attribute) (gxformat2.schema.gxformat2_strict.MinMax attribute) min (gxformat2.schema.gxformat2.MinMax attribute) (gxformat2.schema.gxformat2_strict.MinMax attribute) MinMax (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) model_config (gxformat2.cytoscape.CytoscapeEdge attribute) (gxformat2.cytoscape.CytoscapeEdgeData attribute) (gxformat2.cytoscape.CytoscapeElements attribute) (gxformat2.cytoscape.CytoscapeLayout attribute) (gxformat2.cytoscape.CytoscapeNode attribute) (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.CytoscapePosition attribute) (gxformat2.cytoscape.models.CytoscapeEdge attribute) (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeElements attribute) (gxformat2.cytoscape.models.CytoscapeLayout attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapePosition attribute) (gxformat2.examples.CatalogEntry attribute) (gxformat2.lint_profiles.LintProfile attribute) (gxformat2.normalized.ExpandedFormat2 attribute) (gxformat2.normalized.ExpandedNativeStep attribute) (gxformat2.normalized.ExpandedNativeWorkflow attribute) (gxformat2.normalized.ExpandedWorkflowStep attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.ArraySchema attribute) (gxformat2.schema.gxformat2.BaseComment attribute) (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.BaseInputParameter attribute) (gxformat2.schema.gxformat2.CreatorOrganization attribute) (gxformat2.schema.gxformat2.CreatorPerson attribute) (gxformat2.schema.gxformat2.Documented attribute) (gxformat2.schema.gxformat2.EnumSchema attribute) (gxformat2.schema.gxformat2.FrameComment attribute) (gxformat2.schema.gxformat2.FreehandComment attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2.HasStepErrors attribute) (gxformat2.schema.gxformat2.HasStepPosition attribute) (gxformat2.schema.gxformat2.HasUUID attribute) (gxformat2.schema.gxformat2.Identified attribute) (gxformat2.schema.gxformat2.InputParameter attribute) (gxformat2.schema.gxformat2.Labeled attribute) (gxformat2.schema.gxformat2.MarkdownComment attribute) (gxformat2.schema.gxformat2.MinMax attribute) (gxformat2.schema.gxformat2.OutputParameter attribute) (gxformat2.schema.gxformat2.Parameter attribute) (gxformat2.schema.gxformat2.Process attribute) (gxformat2.schema.gxformat2.RecordField attribute) (gxformat2.schema.gxformat2.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2.RecordSchema attribute) (gxformat2.schema.gxformat2.ReferencesTool attribute) (gxformat2.schema.gxformat2.Report attribute) (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2.Sink attribute) (gxformat2.schema.gxformat2.StepPosition attribute) (gxformat2.schema.gxformat2.TextComment attribute) (gxformat2.schema.gxformat2.ToolShedRepository attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStepInput attribute) (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2.WorkflowTextOption attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.ArraySchema attribute) (gxformat2.schema.gxformat2_strict.BaseComment attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.BaseInputParameter attribute) (gxformat2.schema.gxformat2_strict.CreatorOrganization attribute) (gxformat2.schema.gxformat2_strict.CreatorPerson attribute) (gxformat2.schema.gxformat2_strict.Documented attribute) (gxformat2.schema.gxformat2_strict.EnumSchema attribute) (gxformat2.schema.gxformat2_strict.FrameComment attribute) (gxformat2.schema.gxformat2_strict.FreehandComment attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.HasStepErrors attribute) (gxformat2.schema.gxformat2_strict.HasStepPosition attribute) (gxformat2.schema.gxformat2_strict.HasUUID attribute) (gxformat2.schema.gxformat2_strict.Identified attribute) (gxformat2.schema.gxformat2_strict.InputParameter attribute) (gxformat2.schema.gxformat2_strict.Labeled attribute) (gxformat2.schema.gxformat2_strict.MarkdownComment attribute) (gxformat2.schema.gxformat2_strict.MinMax attribute) (gxformat2.schema.gxformat2_strict.OutputParameter attribute) (gxformat2.schema.gxformat2_strict.Parameter attribute) (gxformat2.schema.gxformat2_strict.Process attribute) (gxformat2.schema.gxformat2_strict.RecordField attribute) (gxformat2.schema.gxformat2_strict.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2_strict.RecordSchema attribute) (gxformat2.schema.gxformat2_strict.ReferencesTool attribute) (gxformat2.schema.gxformat2_strict.Report attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.Sink attribute) (gxformat2.schema.gxformat2_strict.StepPosition attribute) (gxformat2.schema.gxformat2_strict.TextComment attribute) (gxformat2.schema.gxformat2_strict.ToolShedRepository attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepInput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextOption attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.ArraySchema attribute) (gxformat2.schema.native.BaseNativeComment attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native.Documented attribute) (gxformat2.schema.native.EnumSchema attribute) (gxformat2.schema.native.HasStepErrors attribute) (gxformat2.schema.native.HasStepPosition attribute) (gxformat2.schema.native.HasUUID attribute) (gxformat2.schema.native.NativeCreatorOrganization attribute) (gxformat2.schema.native.NativeCreatorPerson attribute) (gxformat2.schema.native.NativeFrameComment attribute) (gxformat2.schema.native.NativeFrameCommentData attribute) (gxformat2.schema.native.NativeFreehandComment attribute) (gxformat2.schema.native.NativeFreehandCommentData attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native.NativeInputConnection attribute) (gxformat2.schema.native.NativeMarkdownComment attribute) (gxformat2.schema.native.NativeMarkdownCommentData attribute) (gxformat2.schema.native.NativePostJobAction attribute) (gxformat2.schema.native.NativeReport attribute) (gxformat2.schema.native.NativeSourceMetadata attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native.NativeStepInput attribute) (gxformat2.schema.native.NativeStepOutput attribute) (gxformat2.schema.native.NativeTextComment attribute) (gxformat2.schema.native.NativeTextCommentData attribute) (gxformat2.schema.native.NativeWorkflowOutput attribute) (gxformat2.schema.native.RecordField attribute) (gxformat2.schema.native.RecordFieldDefinition attribute) (gxformat2.schema.native.RecordSchema attribute) (gxformat2.schema.native.ReferencesTool attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native.StepPosition attribute) (gxformat2.schema.native.ToolShedRepository attribute) (gxformat2.schema.native.WorkflowTextOption attribute) (gxformat2.schema.native_strict.ArraySchema attribute) (gxformat2.schema.native_strict.BaseNativeComment attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) (gxformat2.schema.native_strict.Documented attribute) (gxformat2.schema.native_strict.EnumSchema attribute) (gxformat2.schema.native_strict.HasStepErrors attribute) (gxformat2.schema.native_strict.HasStepPosition attribute) (gxformat2.schema.native_strict.HasUUID attribute) (gxformat2.schema.native_strict.NativeCreatorOrganization attribute) (gxformat2.schema.native_strict.NativeCreatorPerson attribute) (gxformat2.schema.native_strict.NativeFrameComment attribute) (gxformat2.schema.native_strict.NativeFrameCommentData attribute) (gxformat2.schema.native_strict.NativeFreehandComment attribute) (gxformat2.schema.native_strict.NativeFreehandCommentData attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeInputConnection attribute) (gxformat2.schema.native_strict.NativeMarkdownComment attribute) (gxformat2.schema.native_strict.NativeMarkdownCommentData attribute) (gxformat2.schema.native_strict.NativePostJobAction attribute) (gxformat2.schema.native_strict.NativeReport attribute) (gxformat2.schema.native_strict.NativeSourceMetadata attribute) (gxformat2.schema.native_strict.NativeStep attribute) (gxformat2.schema.native_strict.NativeStepInput attribute) (gxformat2.schema.native_strict.NativeStepOutput attribute) (gxformat2.schema.native_strict.NativeTextComment attribute) (gxformat2.schema.native_strict.NativeTextCommentData attribute) (gxformat2.schema.native_strict.NativeWorkflowOutput attribute) (gxformat2.schema.native_strict.RecordField attribute) (gxformat2.schema.native_strict.RecordFieldDefinition attribute) (gxformat2.schema.native_strict.RecordSchema attribute) (gxformat2.schema.native_strict.ReferencesTool attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.StepPosition attribute) (gxformat2.schema.native_strict.ToolShedRepository attribute) (gxformat2.schema.native_strict.WorkflowTextOption attribute) (gxformat2.schema_rules.SchemaRule attribute) (gxformat2.schema_rules.SchemaRuleTests attribute) (gxformat2.testing.Assertion attribute) (gxformat2.testing.ExpectationSuite attribute) (gxformat2.testing.TestCase attribute)

module gxformat2 gxformat2.abstract gxformat2.converter gxformat2.cytoscape gxformat2.cytoscape.models gxformat2.examples gxformat2.export gxformat2.interface gxformat2.lint gxformat2.lint_profiles gxformat2.lint_rules gxformat2.linting gxformat2.markdown_parse gxformat2.mermaid gxformat2.model gxformat2.normalize gxformat2.normalized gxformat2.options gxformat2.schema gxformat2.schema.gxformat2 gxformat2.schema.gxformat2_strict gxformat2.schema.json_schema gxformat2.schema.native gxformat2.schema.native_strict gxformat2.schema.native_v0_1 gxformat2.schema.v19_09 gxformat2.schema_rules gxformat2.testing gxformat2.validators gxformat2.yaml

N

name (gxformat2.cytoscape.CytoscapeLayout attribute) (gxformat2.cytoscape.models.CytoscapeLayout attribute) (gxformat2.examples.CatalogEntry property) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2.RecordField attribute) (gxformat2.schema.gxformat2.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2.ToolShedRepository attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.RecordField attribute) (gxformat2.schema.gxformat2_strict.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.ToolShedRepository attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native.NativeStepInput attribute) (gxformat2.schema.native.NativeStepOutput attribute) (gxformat2.schema.native.RecordField attribute) (gxformat2.schema.native.RecordFieldDefinition attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native.ToolShedRepository attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeStep attribute) (gxformat2.schema.native_strict.NativeStepInput attribute) (gxformat2.schema.native_strict.NativeStepOutput attribute) (gxformat2.schema.native_strict.RecordField attribute) (gxformat2.schema.native_strict.RecordFieldDefinition attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.ToolShedRepository attribute) (gxformat2.schema.native_v0_1.NativeCreatorOrganization attribute) (gxformat2.schema.native_v0_1.NativeCreatorPerson attribute) (gxformat2.schema.native_v0_1.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_v0_1.NativeStep attribute) (gxformat2.schema.native_v0_1.NativeStepInput attribute) (gxformat2.schema.native_v0_1.NativeStepOutput attribute) (gxformat2.schema.native_v0_1.RecordField attribute) (gxformat2.schema.native_v0_1.RecordFieldDefinition attribute) (gxformat2.schema.native_v0_1.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_v0_1.ToolShedRepository attribute) (gxformat2.schema.v19_09.CreatorOrganization attribute) (gxformat2.schema.v19_09.CreatorPerson attribute) (gxformat2.schema.v19_09.RecordField attribute) (gxformat2.schema.v19_09.RecordFieldDefinition attribute) (gxformat2.schema.v19_09.SampleSheetColumnDefinition attribute) (gxformat2.schema.v19_09.ToolShedRepository attribute) namespaces (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) native (gxformat2.examples.ExampleFormat attribute) (gxformat2.schema_rules.AppliesTo attribute) native_input_to_format2_type() (in module gxformat2.normalized) native_workflow_json_schema() (in module gxformat2.schema.json_schema) native_workflow_json_schema_string() (in module gxformat2.schema.json_schema) NativeCreatorOrganization (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeCreatorOrganizationTypeLoader (in module gxformat2.schema.native_v0_1) NativeCreatorPerson (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeCreatorPersonTypeLoader (in module gxformat2.schema.native_v0_1) NativeFrameComment (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeFrameCommentData (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1)

NativeFreehandComment (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeFreehandCommentData (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeGalaxyWorkflow (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeInputConnection (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeMarkdownComment (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeMarkdownCommentData (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativePostJobAction (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeReport (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeSourceMetadata (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeStep (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeStepInput (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeStepKeyNotInteger (class in gxformat2.lint_rules) NativeStepOutput (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeStepType (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) NativeStepTypeLoader (in module gxformat2.schema.native_v0_1) NativeTextComment (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeTextCommentData (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) NativeWorkflowOutput (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) navigate() (in module gxformat2.testing) negative (gxformat2.schema_rules.SchemaRuleTests attribute) no_link_check (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) nodes (gxformat2.cytoscape.CytoscapeElements attribute) (gxformat2.cytoscape.models.CytoscapeElements attribute) normalized_format2() (in module gxformat2.normalized) normalized_native() (in module gxformat2.normalized) NormalizedFormat2 (class in gxformat2.normalized) NormalizedNativeStep (class in gxformat2.normalized) NormalizedNativeWorkflow (class in gxformat2.normalized) NormalizedWorkflowStep (class in gxformat2.normalized) null (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute)

O

operation (gxformat2.testing.TestCase attribute) optional (gxformat2.schema.gxformat2.BaseInputParameter attribute) (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.BaseInputParameter attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) ordered_dump() (in module gxformat2.yaml) ordered_dump_to_path() (in module gxformat2.yaml) ordered_load() (in module gxformat2.yaml) ordered_load_path() (in module gxformat2.yaml) origin (gxformat2.examples.CatalogEntry attribute) original_doc (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) out (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) output (gxformat2.cytoscape.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeEdgeData attribute)

output_name (gxformat2.normalized.SourceReference attribute) (gxformat2.schema.native.NativeInputConnection attribute) (gxformat2.schema.native.NativePostJobAction attribute) (gxformat2.schema.native.NativeWorkflowOutput attribute) (gxformat2.schema.native_strict.NativeInputConnection attribute) (gxformat2.schema.native_strict.NativePostJobAction attribute) (gxformat2.schema.native_strict.NativeWorkflowOutput attribute) OutputParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) outputs (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.gxformat2.Process attribute) (gxformat2.schema.gxformat2_strict.Process attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) outputs() (in module gxformat2.normalize) outputs_normalized() (in module gxformat2.normalize) outputSource (gxformat2.schema.gxformat2.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowOutputParameter attribute) owner (gxformat2.schema.gxformat2.ToolShedRepository attribute) (gxformat2.schema.gxformat2_strict.ToolShedRepository attribute) (gxformat2.schema.native.ToolShedRepository attribute) (gxformat2.schema.native_strict.ToolShedRepository attribute)

P

Parameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) parameter_input (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStepType attribute) parse_errors() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) parser_info() (in module gxformat2.schema.gxformat2) (in module gxformat2.schema.gxformat2_strict) (in module gxformat2.schema.native) (in module gxformat2.schema.native_strict) (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) path (gxformat2.examples.CatalogEntry property) (gxformat2.testing.Assertion attribute) pause (gxformat2.schema.gxformat2.WorkflowStepType attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepType attribute) (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStepType attribute) pick_value (gxformat2.schema.gxformat2.WorkflowStepType attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepType attribute) (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStepType attribute) position (gxformat2.cytoscape.CytoscapeNode attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.BaseComment attribute) (gxformat2.schema.gxformat2.BaseDataParameter attribute) (gxformat2.schema.gxformat2.HasStepPosition attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.BaseComment attribute) (gxformat2.schema.gxformat2_strict.BaseDataParameter attribute) (gxformat2.schema.gxformat2_strict.HasStepPosition attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.BaseNativeComment attribute) (gxformat2.schema.native.HasStepPosition attribute) (gxformat2.schema.native_strict.BaseNativeComment attribute) (gxformat2.schema.native_strict.HasStepPosition attribute)

positive (gxformat2.schema_rules.SchemaRuleTests attribute) post_job_actions (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) prefix_url() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) PrimitiveType (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) PrimitiveTypeLoader (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) print_messages() (gxformat2.linting.LintContext method) Process (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) profile (gxformat2.lint_rules.NativeStepKeyNotInteger attribute) (gxformat2.linting.Linter attribute) pytest_params() (gxformat2.testing.DeclarativeTestSuite method) python_to_workflow() (in module gxformat2) (in module gxformat2.converter)

R

readme (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) real (gxformat2.examples.ExampleOrigin attribute) real_hacked (gxformat2.examples.ExampleOrigin attribute) RecordField (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) RecordFieldDefinition (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) RecordSchema (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) ReferencesTool (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) release (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) remove_tags (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) rename (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) render_html() (in module gxformat2.cytoscape)

repo_link (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) Report (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) report (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) resolve_source() (gxformat2.normalized.NormalizedFormat2 method) resolve_source_reference() (in module gxformat2.model) (in module gxformat2.normalized) restrictions (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) restrictOnConnections (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) root (gxformat2.testing.ExpectationSuite attribute) rules (gxformat2.lint_profiles.LintProfile attribute) rules_for_profile() (in module gxformat2.lint_profiles) run (gxformat2.normalized.ExpandedWorkflowStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) run() (gxformat2.testing.DeclarativeTestSuite method) run_assertion() (in module gxformat2.testing) run_declarative_case() (in module gxformat2.testing) runtime_inputs (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) rvocab (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute)

S

SampleSheetColumnDefinition (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) save() (gxformat2.schema.native_v0_1.ArraySchema method) (gxformat2.schema.native_v0_1.EnumSchema method) (gxformat2.schema.native_v0_1.NativeCreatorOrganization method) (gxformat2.schema.native_v0_1.NativeCreatorPerson method) (gxformat2.schema.native_v0_1.NativeFrameComment method) (gxformat2.schema.native_v0_1.NativeFrameCommentData method) (gxformat2.schema.native_v0_1.NativeFreehandComment method) (gxformat2.schema.native_v0_1.NativeFreehandCommentData method) (gxformat2.schema.native_v0_1.NativeGalaxyWorkflow method) (gxformat2.schema.native_v0_1.NativeInputConnection method) (gxformat2.schema.native_v0_1.NativeMarkdownComment method) (gxformat2.schema.native_v0_1.NativeMarkdownCommentData method) (gxformat2.schema.native_v0_1.NativePostJobAction method) (gxformat2.schema.native_v0_1.NativeReport method) (gxformat2.schema.native_v0_1.NativeSourceMetadata method) (gxformat2.schema.native_v0_1.NativeStep method) (gxformat2.schema.native_v0_1.NativeStepInput method) (gxformat2.schema.native_v0_1.NativeStepOutput method) (gxformat2.schema.native_v0_1.NativeTextComment method) (gxformat2.schema.native_v0_1.NativeTextCommentData method) (gxformat2.schema.native_v0_1.NativeWorkflowOutput method) (gxformat2.schema.native_v0_1.RecordField method) (gxformat2.schema.native_v0_1.RecordFieldDefinition method) (gxformat2.schema.native_v0_1.RecordSchema method) (gxformat2.schema.native_v0_1.SampleSheetColumnDefinition method) (gxformat2.schema.native_v0_1.Saveable method) (gxformat2.schema.native_v0_1.StepPosition method) (gxformat2.schema.native_v0_1.ToolShedRepository method) (gxformat2.schema.native_v0_1.WorkflowTextOption method) (gxformat2.schema.v19_09.ArraySchema method) (gxformat2.schema.v19_09.BaseDataParameter method) (gxformat2.schema.v19_09.BaseInputParameter method) (gxformat2.schema.v19_09.CreatorOrganization method) (gxformat2.schema.v19_09.CreatorPerson method) (gxformat2.schema.v19_09.EnumSchema method) (gxformat2.schema.v19_09.FrameComment method) (gxformat2.schema.v19_09.FreehandComment method) (gxformat2.schema.v19_09.GalaxyWorkflow method) (gxformat2.schema.v19_09.MarkdownComment method) (gxformat2.schema.v19_09.MinMax method) (gxformat2.schema.v19_09.RecordField method) (gxformat2.schema.v19_09.RecordFieldDefinition method) (gxformat2.schema.v19_09.RecordSchema method) (gxformat2.schema.v19_09.Report method) (gxformat2.schema.v19_09.SampleSheetColumnDefinition method) (gxformat2.schema.v19_09.Saveable method) (gxformat2.schema.v19_09.StepPosition method) (gxformat2.schema.v19_09.TextComment method) (gxformat2.schema.v19_09.ToolShedRepository method) (gxformat2.schema.v19_09.WorkflowBooleanParameter method) (gxformat2.schema.v19_09.WorkflowCollectionParameter method) (gxformat2.schema.v19_09.WorkflowDataParameter method) (gxformat2.schema.v19_09.WorkflowFloatParameter method) (gxformat2.schema.v19_09.WorkflowInputParameter method) (gxformat2.schema.v19_09.WorkflowIntegerParameter method) (gxformat2.schema.v19_09.WorkflowOutputParameter method) (gxformat2.schema.v19_09.WorkflowStep method) (gxformat2.schema.v19_09.WorkflowStepInput method) (gxformat2.schema.v19_09.WorkflowStepOutput method) (gxformat2.schema.v19_09.WorkflowTextOption method) (gxformat2.schema.v19_09.WorkflowTextParameter method) (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) save_relative_uri() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) save_with_metadata() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) Saveable (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) SchemaRule (class in gxformat2.schema_rules) SchemaRuleTests (class in gxformat2.schema_rules) schemas (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute) Scope (class in gxformat2.schema_rules) scope (gxformat2.schema_rules.SchemaRule attribute)

set_columns (gxformat2.schema.gxformat2.WorkflowStepOutput attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepOutput attribute) setup_connected_values() (in module gxformat2.model) Severity (class in gxformat2.schema_rules) severity (gxformat2.lint_rules.NativeStepKeyNotInteger attribute) (gxformat2.linting.Linter attribute) (gxformat2.schema_rules.SchemaRule attribute) shortname() (in module gxformat2.schema.native_v0_1) (in module gxformat2.schema.v19_09) Sink (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) size (gxformat2.schema.gxformat2.BaseComment attribute) (gxformat2.schema.gxformat2_strict.BaseComment attribute) (gxformat2.schema.native.BaseNativeComment attribute) (gxformat2.schema.native.NativeTextCommentData attribute) (gxformat2.schema.native_strict.BaseNativeComment attribute) (gxformat2.schema.native_strict.NativeTextCommentData attribute) source (gxformat2.cytoscape.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) (gxformat2.schema.gxformat2.Sink attribute) (gxformat2.schema.gxformat2_strict.Sink attribute) source_metadata (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) SourceReference (class in gxformat2.normalized) state (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) StateEncodeToFormat2Fn (in module gxformat2.options) StateEncodeToNativeFn (in module gxformat2.options) step_label (gxformat2.normalized.SourceReference attribute) step_type (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) StepPosition (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) steps (gxformat2.normalized.ExpandedFormat2 attribute) (gxformat2.normalized.ExpandedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) steps() (in module gxformat2.normalize) steps_as_list() (in module gxformat2.model) steps_normalized() (in module gxformat2.normalize) strict (gxformat2.schema_rules.Scope attribute) string (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.PrimitiveType attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.PrimitiveType attribute) (gxformat2.schema.native.PrimitiveType attribute) (gxformat2.schema.native_strict.PrimitiveType attribute) subworkflow (gxformat2.normalized.ExpandedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.gxformat2.WorkflowStepType attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepType attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStep attribute) (gxformat2.schema.native_strict.NativeStepType attribute) subworkflows (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) suggestions (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) symbols (gxformat2.schema.gxformat2.EnumSchema attribute) (gxformat2.schema.gxformat2_strict.EnumSchema attribute) (gxformat2.schema.native.EnumSchema attribute) (gxformat2.schema.native_strict.EnumSchema attribute) synthetic (gxformat2.examples.ExampleOrigin attribute)

T

tags (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.gxformat2.GalaxyWorkflow attribute) (gxformat2.schema.gxformat2_strict.GalaxyWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) target (gxformat2.cytoscape.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) telephone (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) TestCase (class in gxformat2.testing) tests (gxformat2.examples.CatalogEntry attribute) (gxformat2.schema_rules.SchemaRule attribute) text (gxformat2.schema.gxformat2.GalaxyType attribute) (gxformat2.schema.gxformat2.MarkdownComment attribute) (gxformat2.schema.gxformat2.TextComment attribute) (gxformat2.schema.gxformat2_strict.GalaxyType attribute) (gxformat2.schema.gxformat2_strict.MarkdownComment attribute) (gxformat2.schema.gxformat2_strict.TextComment attribute) (gxformat2.schema.native.NativeMarkdownCommentData attribute) (gxformat2.schema.native.NativeTextCommentData attribute) (gxformat2.schema.native_strict.NativeMarkdownCommentData attribute) (gxformat2.schema.native_strict.NativeTextCommentData attribute) text_size (gxformat2.schema.gxformat2.TextComment attribute) (gxformat2.schema.gxformat2_strict.TextComment attribute) TextComment (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) thickness (gxformat2.schema.gxformat2.FreehandComment attribute) (gxformat2.schema.gxformat2_strict.FreehandComment attribute) (gxformat2.schema.native.NativeFreehandCommentData attribute) (gxformat2.schema.native_strict.NativeFreehandCommentData attribute) title (gxformat2.schema.gxformat2.FrameComment attribute) (gxformat2.schema.gxformat2_strict.FrameComment attribute) (gxformat2.schema.native.NativeFrameCommentData attribute) (gxformat2.schema.native_strict.NativeFrameCommentData attribute) to_cytoscape() (in module gxformat2.cytoscape) to_dict() (gxformat2.cytoscape.CytoscapeElements method) (gxformat2.cytoscape.models.CytoscapeElements method) to_format2() (in module gxformat2) (in module gxformat2.normalized) to_list() (gxformat2.cytoscape.CytoscapeElements method) (gxformat2.cytoscape.models.CytoscapeElements method) to_mermaid() (in module gxformat2.mermaid) to_native() (in module gxformat2) (in module gxformat2.normalized) tool (gxformat2.schema.gxformat2.WorkflowStepType attribute) (gxformat2.schema.gxformat2_strict.WorkflowStepType attribute) (gxformat2.schema.native.NativeStepType attribute) (gxformat2.schema.native_strict.NativeStepType attribute) tool_id (gxformat2.cytoscape.CytoscapeNodeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.normalized.ToolReference attribute) (gxformat2.schema.gxformat2.ReferencesTool attribute) (gxformat2.schema.gxformat2_strict.ReferencesTool attribute) (gxformat2.schema.native.ReferencesTool attribute) (gxformat2.schema.native_strict.ReferencesTool attribute) tool_representation (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) tool_shed (gxformat2.schema.gxformat2.ToolShedRepository attribute) (gxformat2.schema.gxformat2_strict.ToolShedRepository attribute) (gxformat2.schema.native.ToolShedRepository attribute) (gxformat2.schema.native_strict.ToolShedRepository attribute) tool_shed_repository (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.ReferencesTool attribute) (gxformat2.schema.gxformat2_strict.ReferencesTool attribute) (gxformat2.schema.native.ReferencesTool attribute) (gxformat2.schema.native_strict.ReferencesTool attribute) tool_state (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) tool_uuid (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) tool_version (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.normalized.ToolReference attribute) (gxformat2.schema.gxformat2.ReferencesTool attribute) (gxformat2.schema.gxformat2_strict.ReferencesTool attribute) (gxformat2.schema.native.ReferencesTool attribute) (gxformat2.schema.native_strict.ReferencesTool attribute)

ToolReference (class in gxformat2.normalized) ToolShedRepository (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) top (gxformat2.schema.gxformat2.StepPosition attribute) (gxformat2.schema.gxformat2_strict.StepPosition attribute) (gxformat2.schema.native.StepPosition attribute) (gxformat2.schema.native_strict.StepPosition attribute) topological_positions() (in module gxformat2.cytoscape) trs_server (gxformat2.schema.native.NativeSourceMetadata attribute) (gxformat2.schema.native_strict.NativeSourceMetadata attribute) trs_tool_id (gxformat2.schema.native.NativeSourceMetadata attribute) (gxformat2.schema.native_strict.NativeSourceMetadata attribute) trs_url (gxformat2.schema.native.NativeSourceMetadata attribute) (gxformat2.schema.native_strict.NativeSourceMetadata attribute) trs_version_id (gxformat2.schema.native.NativeSourceMetadata attribute) (gxformat2.schema.native_strict.NativeSourceMetadata attribute) type_ (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.ArraySchema attribute) (gxformat2.schema.gxformat2.EnumSchema attribute) (gxformat2.schema.gxformat2.FrameComment attribute) (gxformat2.schema.gxformat2.FreehandComment attribute) (gxformat2.schema.gxformat2.MarkdownComment attribute) (gxformat2.schema.gxformat2.RecordField attribute) (gxformat2.schema.gxformat2.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2.RecordSchema attribute) (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2.TextComment attribute) (gxformat2.schema.gxformat2.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowTextParameter attribute) (gxformat2.schema.gxformat2_strict.ArraySchema attribute) (gxformat2.schema.gxformat2_strict.EnumSchema attribute) (gxformat2.schema.gxformat2_strict.FrameComment attribute) (gxformat2.schema.gxformat2_strict.FreehandComment attribute) (gxformat2.schema.gxformat2_strict.MarkdownComment attribute) (gxformat2.schema.gxformat2_strict.RecordField attribute) (gxformat2.schema.gxformat2_strict.RecordFieldDefinition attribute) (gxformat2.schema.gxformat2_strict.RecordSchema attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.TextComment attribute) (gxformat2.schema.gxformat2_strict.WorkflowBooleanParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowCollectionParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowDataParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowFloatParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowInputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowIntegerParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowOutputParameter attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextParameter attribute) (gxformat2.schema.native.ArraySchema attribute) (gxformat2.schema.native.EnumSchema attribute) (gxformat2.schema.native.NativeFrameComment attribute) (gxformat2.schema.native.NativeFreehandComment attribute) (gxformat2.schema.native.NativeMarkdownComment attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native.NativeStepOutput attribute) (gxformat2.schema.native.NativeTextComment attribute) (gxformat2.schema.native.RecordField attribute) (gxformat2.schema.native.RecordFieldDefinition attribute) (gxformat2.schema.native.RecordSchema attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.ArraySchema attribute) (gxformat2.schema.native_strict.EnumSchema attribute) (gxformat2.schema.native_strict.NativeFrameComment attribute) (gxformat2.schema.native_strict.NativeFreehandComment attribute) (gxformat2.schema.native_strict.NativeMarkdownComment attribute) (gxformat2.schema.native_strict.NativeStep attribute) (gxformat2.schema.native_strict.NativeStepOutput attribute) (gxformat2.schema.native_strict.NativeTextComment attribute) (gxformat2.schema.native_strict.RecordField attribute) (gxformat2.schema.native_strict.RecordFieldDefinition attribute) (gxformat2.schema.native_strict.RecordSchema attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute)

U

unique_tools (gxformat2.normalized.NormalizedFormat2 property) (gxformat2.normalized.NormalizedNativeWorkflow property) url (gxformat2.schema.gxformat2.BaseCreator attribute) (gxformat2.schema.gxformat2_strict.BaseCreator attribute) (gxformat2.schema.native.BaseNativeCreator attribute) (gxformat2.schema.native.NativeSourceMetadata attribute) (gxformat2.schema.native_strict.BaseNativeCreator attribute) (gxformat2.schema.native_strict.NativeSourceMetadata attribute) UrlResolverFn (in module gxformat2.options)

uuid (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.HasUUID attribute) (gxformat2.schema.gxformat2_strict.HasUUID attribute) (gxformat2.schema.native.HasUUID attribute) (gxformat2.schema.native.NativeWorkflowOutput attribute) (gxformat2.schema.native_strict.HasUUID attribute) (gxformat2.schema.native_strict.NativeWorkflowOutput attribute)

V

validate_format2() (in module gxformat2.validators) validate_format2_strict() (in module gxformat2.validators) validate_galaxy_markdown() (in module gxformat2.markdown_parse) validate_native() (in module gxformat2.validators) validate_native_strict() (in module gxformat2.validators) validator_for_fixture() (in module gxformat2.validators) validators (gxformat2.schema.gxformat2.SampleSheetColumnDefinition attribute) (gxformat2.schema.gxformat2_strict.SampleSheetColumnDefinition attribute) (gxformat2.schema.native.SampleSheetColumnDefinition attribute) (gxformat2.schema.native_strict.SampleSheetColumnDefinition attribute) value (gxformat2.schema.gxformat2.WorkflowTextOption attribute) (gxformat2.schema.gxformat2_strict.WorkflowTextOption attribute) (gxformat2.schema.native.WorkflowTextOption attribute) (gxformat2.schema.native_strict.WorkflowTextOption attribute) (gxformat2.testing.Assertion attribute)

value_absent (gxformat2.testing.Assertion attribute) value_any_contains (gxformat2.testing.Assertion attribute) value_contains (gxformat2.testing.Assertion attribute) value_falsy (gxformat2.testing.Assertion attribute) value_matches (gxformat2.testing.Assertion attribute) value_set (gxformat2.testing.Assertion attribute) value_truthy (gxformat2.testing.Assertion attribute) value_type (gxformat2.testing.Assertion attribute) version (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.schema.native.NativeGalaxyWorkflow attribute) (gxformat2.schema.native_strict.NativeGalaxyWorkflow attribute) vocab (gxformat2.schema.native_v0_1.LoadingOptions attribute) (gxformat2.schema.v19_09.LoadingOptions attribute)

W

WARN (gxformat2.linting.LintLevel attribute) warn() (gxformat2.linting.LintContext method) warn_messages (gxformat2.linting.LintContext attribute) warning (gxformat2.schema_rules.Severity attribute) when (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.schema.gxformat2.WorkflowStep attribute) (gxformat2.schema.gxformat2_strict.WorkflowStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) workflow_annotation (gxformat2.examples.CatalogEntry property) workflow_json_schema() (in module gxformat2.schema.json_schema) workflow_json_schema_string() (in module gxformat2.schema.json_schema) workflow_label (gxformat2.examples.CatalogEntry property) workflow_outputs (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.schema.native.NativeStep attribute) (gxformat2.schema.native_strict.NativeStep attribute) workflow_to_mermaid() (in module gxformat2.mermaid) WorkflowBooleanParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowCollectionParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowDataParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowFloatParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09)

WorkflowInputParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowIntegerParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowOutputParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowStep (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowStepInput (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowStepOutput (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09) WorkflowStepType (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) WorkflowStepTypeLoader (in module gxformat2.schema.v19_09) WorkflowTextOption (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.native) (class in gxformat2.schema.native_strict) (class in gxformat2.schema.native_v0_1) (class in gxformat2.schema.v19_09) WorkflowTextParameter (class in gxformat2.schema.gxformat2) (class in gxformat2.schema.gxformat2_strict) (class in gxformat2.schema.v19_09)

X

x (gxformat2.cytoscape.CytoscapePosition attribute) (gxformat2.cytoscape.models.CytoscapePosition attribute)

Y

y (gxformat2.cytoscape.CytoscapePosition attribute) (gxformat2.cytoscape.models.CytoscapePosition attribute)

yaml_to_workflow() (in module gxformat2.converter)