Index

A

a_galaxy_workflow (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) addl_metadata (gxformat2.schema.v19_09.LoadingOptions attribute) ALL (gxformat2.linting.LintLevel attribute) annotation (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) AnyLoader (in module gxformat2.schema.v19_09) applies_to (gxformat2.linting.Linter attribute) ArraySchema (class in gxformat2.schema.v19_09) attrs (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), [1] BaseComment (class in gxformat2.schema.v19_09) BaseCreator (class in gxformat2.schema.v19_09)

BaseDataParameter (class in gxformat2.schema.v19_09) BaseInputParameter (class in gxformat2.schema.v19_09) baseuri (gxformat2.schema.v19_09.LoadingOptions attribute) BioBlendImporterGalaxyInterface (class in gxformat2.interface)

C

cache (gxformat2.schema.v19_09.LoadingOptions attribute) CatalogEntry (class in gxformat2.examples) child() (gxformat2.linting.LintContext method) class_ (gxformat2.normalized._format2.GalaxyUserToolStub attribute) (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedFormat2 attribute) classes (gxformat2.cytoscape.CytoscapeNode attribute), [1] (gxformat2.cytoscape.models.CytoscapeNode attribute) comments (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) connected_paths (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) container (gxformat2.schema.v19_09.LoadingOptions attribute) content_id (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) content_source (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) ConversionOptions (class in gxformat2.options) convert_typing() (in module gxformat2.schema.v19_09)

converted (gxformat2.examples.ExampleOrigin attribute) creator (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) CreatorOrganization (class in gxformat2.schema.v19_09) CreatorOrganizationTypeLoader (in module gxformat2.schema.v19_09) CreatorPerson (class in gxformat2.schema.v19_09) CreatorPersonTypeLoader (in module gxformat2.schema.v19_09) cytoscape_elements() (in module gxformat2.cytoscape), [1] CytoscapeEdge (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models) CytoscapeEdgeData (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models) CytoscapeElements (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models) CytoscapeLayout (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models) CytoscapeNode (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models) CytoscapeNodeData (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models) CytoscapePosition (class in gxformat2.cytoscape), [1] (class in gxformat2.cytoscape.models)

D

data (gxformat2.cytoscape.CytoscapeEdge attribute), [1] (gxformat2.cytoscape.CytoscapeNode attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdge attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) default_url_resolver() (in module gxformat2.options) doc (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute)

Documented (class in gxformat2.schema.v19_09) doi (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute)

E

edges (gxformat2.cytoscape.CytoscapeElements attribute), [1] (gxformat2.cytoscape.models.CytoscapeElements 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.v19_09) ERROR (gxformat2.linting.LintLevel attribute) error() (gxformat2.linting.LintContext method) errors (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute)

ExampleFormat (class in gxformat2.examples) ExampleOrigin (class in gxformat2.examples) expand_url() (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) extract_type() (in module gxformat2.schema.v19_09)

F

fetcher (gxformat2.schema.v19_09.LoadingOptions attribute) file (gxformat2.examples.CatalogEntry attribute) file_uri() (in module gxformat2.schema.v19_09) fileuri (gxformat2.schema.v19_09.LoadingOptions attribute) format (gxformat2.examples.CatalogEntry attribute) format2 (gxformat2.examples.ExampleFormat attribute) format_version (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) FrameComment (class in gxformat2.schema.v19_09) FreehandComment (class in gxformat2.schema.v19_09) from_dict() (in module gxformat2.abstract) from_galaxy_native() (in module gxformat2.export) fromDoc() (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

GalaxyTypeLoader (in module gxformat2.schema.v19_09) GalaxyUserToolStub (class in gxformat2.normalized._format2) GalaxyWorkflow (class in gxformat2.schema.v19_09) get_native_step_type() (in module gxformat2.model) get_path() (in module gxformat2.examples) graph (gxformat2.schema.v19_09.LoadingOptions property) group (gxformat2.cytoscape.CytoscapeEdge attribute), [1] (gxformat2.cytoscape.CytoscapeNode attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdge attribute) (gxformat2.cytoscape.models.CytoscapeNode attribute) gxformat2.abstract module gxformat2.converter module gxformat2.cytoscape module, [1] gxformat2.cytoscape.models module gxformat2.examples module gxformat2.export module gxformat2.interface module gxformat2.lint module gxformat2.linting module

gxformat2.markdown_parse module gxformat2.model module gxformat2.normalize module gxformat2.normalized module gxformat2.normalized._expanded module gxformat2.normalized._format2 module gxformat2.normalized._native module gxformat2.options module gxformat2.schema module gxformat2.schema.v19_09 module gxformat2.to_format2 module gxformat2.to_native module gxformat2.yaml module

H

HasStepErrors (class in gxformat2.schema.v19_09) HasStepPosition (class in gxformat2.schema.v19_09)

HasUUID (class in gxformat2.schema.v19_09) help (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute)

I

id (gxformat2.cytoscape.CytoscapeEdgeData attribute), [1] (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep 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) Identified (class in gxformat2.schema.v19_09) idx (gxformat2.schema.v19_09.LoadingOptions attribute) import_path (gxformat2.normalized._format2.ImportReference attribute) import_workflow() (gxformat2.interface.BioBlendImporterGalaxyInterface method) (gxformat2.interface.ImporterGalaxyInterface method) ImporterGalaxyInterface (class in gxformat2.interface) ImportReference (class in gxformat2.normalized._format2) imports (gxformat2.schema.v19_09.LoadingOptions attribute) in_ (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) includes (gxformat2.schema.v19_09.LoadingOptions attribute) inline_tool_class (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property)

inline_tool_representation (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized.NormalizedWorkflowStep property) input (gxformat2.cytoscape.CytoscapeEdgeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) input_connections (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) InputParameter (class in gxformat2.schema.v19_09) inputs (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) inputs() (in module gxformat2.normalize) inputs_normalized() (in module gxformat2.normalize) is_inline_tool_step (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_input_step (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) is_layout_name() (in module gxformat2.cytoscape), [1] is_pause_step (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_pick_value_step (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_subworkflow_step (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_tool_step (gxformat2.normalized._format2.NormalizedWorkflowStep property) (gxformat2.normalized._native.NormalizedNativeStep property) (gxformat2.normalized.NormalizedNativeStep property) (gxformat2.normalized.NormalizedWorkflowStep property) is_trs_url() (in module gxformat2.options)

J

json_pointer (gxformat2.linting.LintMessage attribute)

K

known_labels (gxformat2.normalized._format2.NormalizedFormat2 property) (gxformat2.normalized.NormalizedFormat2 property)

L

label (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) Labeled (class in gxformat2.schema.v19_09) layout (gxformat2.cytoscape.CytoscapeElements attribute), [1] (gxformat2.cytoscape.models.CytoscapeElements attribute) level (gxformat2.linting.LintMessage attribute) license (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow 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_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) 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.v19_09) load_document_by_string() (in module gxformat2.schema.v19_09) load_document_by_yaml() (in module gxformat2.schema.v19_09) load_document_with_metadata() (in module gxformat2.schema.v19_09) load_field() (in module gxformat2.schema.v19_09) load_native() (in module gxformat2.normalized._native) LoadingOptions (class in gxformat2.schema.v19_09) logo_url (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute)

M

main() (in module gxformat2.abstract) (in module gxformat2.converter) (in module gxformat2.cytoscape), [1] (in module gxformat2.export) (in module gxformat2.lint) MarkdownComment (class in gxformat2.schema.v19_09) MinMax (class in gxformat2.schema.v19_09) model_config (gxformat2.cytoscape.CytoscapeEdge attribute), [1] (gxformat2.cytoscape.CytoscapeEdgeData attribute), [1] (gxformat2.cytoscape.CytoscapeElements attribute), [1] (gxformat2.cytoscape.CytoscapeLayout attribute), [1] (gxformat2.cytoscape.CytoscapeNode attribute), [1] (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.CytoscapePosition attribute), [1] (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.normalized._format2.GalaxyUserToolStub attribute) (gxformat2.normalized._format2.ImportReference attribute) (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow 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)

module gxformat2.abstract gxformat2.converter gxformat2.cytoscape, [1] gxformat2.cytoscape.models gxformat2.examples gxformat2.export gxformat2.interface gxformat2.lint gxformat2.linting gxformat2.markdown_parse gxformat2.model gxformat2.normalize gxformat2.normalized gxformat2.normalized._expanded gxformat2.normalized._format2 gxformat2.normalized._native gxformat2.options gxformat2.schema gxformat2.schema.v19_09 gxformat2.to_format2 gxformat2.to_native gxformat2.yaml

N

name (gxformat2.cytoscape.CytoscapeLayout attribute), [1] (gxformat2.cytoscape.models.CytoscapeLayout attribute) (gxformat2.examples.CatalogEntry property) (gxformat2.normalized._format2.GalaxyUserToolStub attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow 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.v19_09.LoadingOptions attribute) native (gxformat2.examples.ExampleFormat attribute)

native_input_to_format2_type() (in module gxformat2.normalized) no_link_check (gxformat2.schema.v19_09.LoadingOptions attribute) nodes (gxformat2.cytoscape.CytoscapeElements attribute), [1] (gxformat2.cytoscape.models.CytoscapeElements attribute) normalized_format2() (in module gxformat2.normalized) (in module gxformat2.normalized._format2) normalized_native() (in module gxformat2.normalized) (in module gxformat2.normalized._native) NormalizedFormat2 (class in gxformat2.normalized) (class in gxformat2.normalized._format2) NormalizedNativeStep (class in gxformat2.normalized) (class in gxformat2.normalized._native) NormalizedNativeWorkflow (class in gxformat2.normalized) (class in gxformat2.normalized._native) NormalizedWorkflowStep (class in gxformat2.normalized) (class in gxformat2.normalized._format2)

O

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.v19_09.LoadingOptions attribute) out (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) output (gxformat2.cytoscape.CytoscapeEdgeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdgeData attribute)

output_name (gxformat2.normalized._format2.SourceReference attribute) (gxformat2.normalized.SourceReference attribute) OutputParameter (class in gxformat2.schema.v19_09) outputs (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) outputs() (in module gxformat2.normalize) outputs_normalized() (in module gxformat2.normalize)

P

Parameter (class in gxformat2.schema.v19_09) parse_errors() (in module gxformat2.schema.v19_09) parser_info() (in module gxformat2.schema.v19_09) path (gxformat2.examples.CatalogEntry property) position (gxformat2.cytoscape.CytoscapeNode attribute), [1] (gxformat2.cytoscape.models.CytoscapeNode attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute)

post_job_actions (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) prefix_url() (in module gxformat2.schema.v19_09) PrimitiveTypeLoader (in module gxformat2.schema.v19_09) print_messages() (gxformat2.linting.LintContext method) Process (class in gxformat2.schema.v19_09) profile (gxformat2.linting.Linter attribute) python_to_workflow() (in module gxformat2.converter)

R

readme (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) real (gxformat2.examples.ExampleOrigin attribute) real_hacked (gxformat2.examples.ExampleOrigin attribute) RecordField (class in gxformat2.schema.v19_09) RecordFieldDefinition (class in gxformat2.schema.v19_09) RecordSchema (class in gxformat2.schema.v19_09) ReferencesTool (class in gxformat2.schema.v19_09) release (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) render_html() (in module gxformat2.cytoscape), [1] repo_link (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeNodeData attribute)

Report (class in gxformat2.schema.v19_09) report (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) resolve_source() (gxformat2.normalized._format2.NormalizedFormat2 method) (gxformat2.normalized.NormalizedFormat2 method) resolve_source_reference() (in module gxformat2.model) (in module gxformat2.normalized) (in module gxformat2.normalized._format2) run (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized.ExpandedWorkflowStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) runtime_inputs (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) rvocab (gxformat2.schema.v19_09.LoadingOptions attribute)

S

SampleSheetColumnDefinition (class in gxformat2.schema.v19_09) save() (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.v19_09) save_relative_uri() (in module gxformat2.schema.v19_09) save_with_metadata() (in module gxformat2.schema.v19_09)

Saveable (class in gxformat2.schema.v19_09) schemas (gxformat2.schema.v19_09.LoadingOptions attribute) setup_connected_values() (in module gxformat2.model) severity (gxformat2.linting.Linter attribute) shortname() (in module gxformat2.schema.v19_09) Sink (class in gxformat2.schema.v19_09) source (gxformat2.cytoscape.CytoscapeEdgeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) source_metadata (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) SourceReference (class in gxformat2.normalized) (class in gxformat2.normalized._format2) state (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) StateEncodeToFormat2Fn (in module gxformat2.options) StateEncodeToNativeFn (in module gxformat2.options) step_label (gxformat2.normalized._format2.SourceReference attribute) (gxformat2.normalized.SourceReference attribute) step_type (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeNodeData attribute) StepPosition (class in gxformat2.schema.v19_09) steps (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.ExpandedFormat2 attribute) (gxformat2.normalized.ExpandedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) steps() (in module gxformat2.normalize) steps_as_list() (in module gxformat2.model) steps_normalized() (in module gxformat2.normalize) subworkflow (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.ExpandedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) subworkflows (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) synthetic (gxformat2.examples.ExampleOrigin attribute)

T

tags (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) target (gxformat2.cytoscape.CytoscapeEdgeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeEdgeData attribute) tests (gxformat2.examples.CatalogEntry attribute) TextComment (class in gxformat2.schema.v19_09) to_cytoscape() (in module gxformat2.cytoscape), [1] to_dict() (gxformat2.cytoscape.CytoscapeElements method), [1] (gxformat2.cytoscape.models.CytoscapeElements method) to_format2() (in module gxformat2.normalized) to_list() (gxformat2.cytoscape.CytoscapeElements method), [1] (gxformat2.cytoscape.models.CytoscapeElements method) to_native() (in module gxformat2.normalized) tool_id (gxformat2.cytoscape.CytoscapeNodeData attribute), [1] (gxformat2.cytoscape.models.CytoscapeNodeData attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.normalized.ToolReference attribute) tool_representation (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute)

tool_shed_repository (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) tool_state (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) tool_uuid (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) tool_version (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) (gxformat2.normalized.ToolReference attribute) ToolReference (class in gxformat2.normalized) ToolShedRepository (class in gxformat2.schema.v19_09) topological_positions() (in module gxformat2.cytoscape), [1] type_ (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute)

U

unique_tools (gxformat2.normalized._format2.NormalizedFormat2 property) (gxformat2.normalized._native.NormalizedNativeWorkflow property) (gxformat2.normalized.NormalizedFormat2 property) (gxformat2.normalized.NormalizedNativeWorkflow property) UrlResolverFn (in module gxformat2.options) uuid (gxformat2.normalized._format2.NormalizedFormat2 attribute) (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedFormat2 attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute)

V

validate_galaxy_markdown() (in module gxformat2.markdown_parse) version (gxformat2.normalized._native.NormalizedNativeWorkflow attribute) (gxformat2.normalized.NormalizedNativeWorkflow attribute)

vocab (gxformat2.schema.v19_09.LoadingOptions attribute)

W

WARN (gxformat2.linting.LintLevel attribute) warn() (gxformat2.linting.LintContext method) when (gxformat2.normalized._format2.NormalizedWorkflowStep attribute) (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedWorkflowStep attribute) workflow_annotation (gxformat2.examples.CatalogEntry property) workflow_label (gxformat2.examples.CatalogEntry property) workflow_outputs (gxformat2.normalized._native.NormalizedNativeStep attribute) (gxformat2.normalized.NormalizedNativeStep attribute) WorkflowBooleanParameter (class in gxformat2.schema.v19_09)

WorkflowCollectionParameter (class in gxformat2.schema.v19_09) WorkflowDataParameter (class in gxformat2.schema.v19_09) WorkflowFloatParameter (class in gxformat2.schema.v19_09) WorkflowInputParameter (class in gxformat2.schema.v19_09) WorkflowIntegerParameter (class in gxformat2.schema.v19_09) WorkflowOutputParameter (class in gxformat2.schema.v19_09) WorkflowStep (class in gxformat2.schema.v19_09) WorkflowStepInput (class in gxformat2.schema.v19_09) WorkflowStepOutput (class in gxformat2.schema.v19_09) WorkflowStepTypeLoader (in module gxformat2.schema.v19_09) WorkflowTextOption (class in gxformat2.schema.v19_09) WorkflowTextParameter (class in gxformat2.schema.v19_09)

X

x (gxformat2.cytoscape.CytoscapePosition attribute), [1] (gxformat2.cytoscape.models.CytoscapePosition attribute)

Y

y (gxformat2.cytoscape.CytoscapePosition attribute), [1] (gxformat2.cytoscape.models.CytoscapePosition attribute)

yaml_to_workflow() (in module gxformat2.converter)