CODE_OF_CONDUCT.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
pyproject.toml
requirements.txt
setup.cfg
gxformat2/__init__.py
gxformat2/_comment_helpers.py
gxformat2/_labels.py
gxformat2/_scripts.py
gxformat2/_semantic_validators.py
gxformat2/_yaml.py
gxformat2/abstract.py
gxformat2/converter.py
gxformat2/export.py
gxformat2/interface.py
gxformat2/lint.py
gxformat2/lint_profiles.py
gxformat2/lint_rules.py
gxformat2/linting.py
gxformat2/markdown_parse.py
gxformat2/model.py
gxformat2/normalize.py
gxformat2/options.py
gxformat2/schema_rules.py
gxformat2/testing.py
gxformat2/validators.py
gxformat2/yaml.py
gxformat2.egg-info/PKG-INFO
gxformat2.egg-info/SOURCES.txt
gxformat2.egg-info/dependency_links.txt
gxformat2.egg-info/entry_points.txt
gxformat2.egg-info/requires.txt
gxformat2.egg-info/top_level.txt
gxformat2/cytoscape/__init__.py
gxformat2/cytoscape/_builder.py
gxformat2/cytoscape/_cli.py
gxformat2/cytoscape/_layout.py
gxformat2/cytoscape/_render.py
gxformat2/cytoscape/cytoscape.html
gxformat2/cytoscape/models.py
gxformat2/examples/__init__.py
gxformat2/examples/catalog.yml
gxformat2/examples/expectations/cytoscape.yml
gxformat2/examples/expectations/ensure_format2.yml
gxformat2/examples/expectations/ensure_native.yml
gxformat2/examples/expectations/lint_best_practices_format2.yml
gxformat2/examples/expectations/lint_best_practices_native.yml
gxformat2/examples/expectations/lint_format2.yml
gxformat2/examples/expectations/lint_native.yml
gxformat2/examples/expectations/mermaid.yml
gxformat2/examples/expectations/normalized_comments.yml
gxformat2/examples/expectations/normalized_format2.yml
gxformat2/examples/expectations/normalized_inputs.yml
gxformat2/examples/expectations/normalized_labels.yml
gxformat2/examples/expectations/normalized_native.yml
gxformat2/examples/expectations/normalized_steps.yml
gxformat2/examples/expectations/post_job_actions.yml
gxformat2/examples/expectations/to_format2.yml
gxformat2/examples/expectations/to_native.yml
gxformat2/examples/expectations/unique_tools.yml
gxformat2/examples/expectations/validate_format2.yml
gxformat2/examples/expectations/validate_native.yml
gxformat2/examples/format2/synthetic-bad-column-default-mismatch.gxwf.yml
gxformat2/examples/format2/synthetic-bad-column-defs-on-list.gxwf.yml
gxformat2/examples/format2/synthetic-bad-fields-on-list.gxwf.yml
gxformat2/examples/format2/synthetic-bad-restrictions-on-data.gxwf.yml
gxformat2/examples/format2/synthetic-basic.gxwf.yml
gxformat2/examples/format2/synthetic-bp-disconnected-input.gxwf.yml
gxformat2/examples/format2/synthetic-bp-no-annotation.gxwf.yml
gxformat2/examples/format2/synthetic-bp-step-no-label.gxwf.yml
gxformat2/examples/format2/synthetic-comments-dict.gxwf.yml
gxformat2/examples/format2/synthetic-comments-list.gxwf.yml
gxformat2/examples/format2/synthetic-doc-array.gxwf.yml
gxformat2/examples/format2/synthetic-extra-field.gxwf.yml
gxformat2/examples/format2/synthetic-float-input-default.gxwf.yml
gxformat2/examples/format2/synthetic-graph-simple.gxwf.yml
gxformat2/examples/format2/synthetic-graph-with-subworkflow.gxwf.yml
gxformat2/examples/format2/synthetic-inner-nested-subworkflow.gxwf.yml
gxformat2/examples/format2/synthetic-inner-subworkflow.gxwf.yml
gxformat2/examples/format2/synthetic-input-shorthand.gxwf.yml
gxformat2/examples/format2/synthetic-input-type-aliases.gxwf.yml
gxformat2/examples/format2/synthetic-inputs-array.gxwf.yml
gxformat2/examples/format2/synthetic-int-input.gxwf.yml
gxformat2/examples/format2/synthetic-int-link.gxwf.yml
gxformat2/examples/format2/synthetic-integer-type-alias.gxwf.yml
gxformat2/examples/format2/synthetic-lint-bad-float-default.gxwf.yml
gxformat2/examples/format2/synthetic-lint-bad-int-default.gxwf.yml
gxformat2/examples/format2/synthetic-lint-bad-output-source.gxwf.yml
gxformat2/examples/format2/synthetic-lint-bad-string-default.gxwf.yml
gxformat2/examples/format2/synthetic-lint-nested-no-steps.gxwf.yml
gxformat2/examples/format2/synthetic-lint-no-class.gxwf.yml
gxformat2/examples/format2/synthetic-lint-report-bad-type.gxwf.yml
gxformat2/examples/format2/synthetic-lint-report.gxwf.yml
gxformat2/examples/format2/synthetic-lint-step-errors.gxwf.yml
gxformat2/examples/format2/synthetic-lint-testtoolshed.gxwf.yml
gxformat2/examples/format2/synthetic-missing-steps.gxwf.yml
gxformat2/examples/format2/synthetic-multi-data-input.gxwf.yml
gxformat2/examples/format2/synthetic-multi-string-input.gxwf.yml
gxformat2/examples/format2/synthetic-multisource-bare-list.gxwf.yml
gxformat2/examples/format2/synthetic-nested-subworkflow.gxwf.yml
gxformat2/examples/format2/synthetic-optional-input.gxwf.yml
gxformat2/examples/format2/synthetic-paired-list-input.gxwf.yml
gxformat2/examples/format2/synthetic-pause-step.gxwf.yml
gxformat2/examples/format2/synthetic-pja-hide-rename.gxwf.yml
gxformat2/examples/format2/synthetic-record-input.gxwf.yml
gxformat2/examples/format2/synthetic-rules-tool.gxwf.yml
gxformat2/examples/format2/synthetic-runtime-inputs.gxwf.yml
gxformat2/examples/format2/synthetic-sample-sheet-input.gxwf.yml
gxformat2/examples/format2/synthetic-single-versioned-tool.gxwf.yml
gxformat2/examples/format2/synthetic-slash-in-input-label.gxwf.yml
gxformat2/examples/format2/synthetic-slash-in-label-chained.gxwf.yml
gxformat2/examples/format2/synthetic-slash-in-step-label.gxwf.yml
gxformat2/examples/format2/synthetic-step-in-shorthand.gxwf.yml
gxformat2/examples/format2/synthetic-step-input-default-file.gxwf.yml
gxformat2/examples/format2/synthetic-step-input-default-scalar.gxwf.yml
gxformat2/examples/format2/synthetic-step-out-shorthand.gxwf.yml
gxformat2/examples/format2/synthetic-step-post-job-actions-merged.gxwf.yml
gxformat2/examples/format2/synthetic-step-post-job-actions.gxwf.yml
gxformat2/examples/format2/synthetic-string-input.gxwf.yml
gxformat2/examples/format2/synthetic-tags.gxwf.yml
gxformat2/examples/format2/synthetic-text-restrict-on-connections.gxwf.yml
gxformat2/examples/format2/synthetic-text-restrictions-options.gxwf.yml
gxformat2/examples/format2/synthetic-text-restrictions.gxwf.yml
gxformat2/examples/format2/synthetic-text-suggestions.gxwf.yml
gxformat2/examples/format2/synthetic-tool-state-json.gxwf.yml
gxformat2/examples/format2/synthetic-tool-with-inline-subworkflow.gxwf.yml
gxformat2/examples/format2/synthetic-unlinted-best-practices.gxwf.yml
gxformat2/examples/format2/synthetic-url-run-yml.gxwf.yml
gxformat2/examples/format2/synthetic-user-defined-tool.gxwf.yml
gxformat2/examples/format2/synthetic-when-step.gxwf.yml
gxformat2/examples/native/real-basic-without-step-input-label.ga
gxformat2/examples/native/real-ecoli-comparison.ga
gxformat2/examples/native/real-hacked-basic-missing-format-version.ga
gxformat2/examples/native/real-hacked-unicycler-assembly-extra-annotations.ga
gxformat2/examples/native/real-hacked-unicycler-assembly-no-tool.ga
gxformat2/examples/native/real-hacked-unicycler-assembly-testtoolshed.ga
gxformat2/examples/native/real-hacked-unicycler-assembly-with-tags.ga
gxformat2/examples/native/real-multi-data-input.ga
gxformat2/examples/native/real-multi-string-input.ga
gxformat2/examples/native/real-sars-cov2-variant-calling.ga
gxformat2/examples/native/real-shed-tools-raw.ga
gxformat2/examples/native/real-unicycler-assembly.ga
gxformat2/examples/native/synthetic-extra-field.ga
gxformat2/examples/native/synthetic-inner-subworkflow.ga
gxformat2/examples/native/synthetic-labeled-tool.ga
gxformat2/examples/native/synthetic-lint-bad-format-version.ga
gxformat2/examples/native/synthetic-lint-bad-marker.ga
gxformat2/examples/native/synthetic-lint-nested-no-steps.ga
gxformat2/examples/native/synthetic-lint-no-steps.ga
gxformat2/examples/native/synthetic-lint-non-integer-step.ga
gxformat2/examples/native/synthetic-lint-output-no-label.ga
gxformat2/examples/native/synthetic-lint-report-bad-type.ga
gxformat2/examples/native/synthetic-lint-report.ga
gxformat2/examples/native/synthetic-minimal-tool.ga
gxformat2/examples/native/synthetic-missing-marker.ga
gxformat2/examples/native/synthetic-native-data-input.ga
gxformat2/examples/native/synthetic-native-tool-with-subworkflow.ga
gxformat2/examples/native/synthetic-outer-inline-subworkflow.ga
gxformat2/examples/native/synthetic-outer-url-subworkflow.ga
gxformat2/examples/native/synthetic-rename-pja.ga
gxformat2/examples/native/synthetic-unlinted-best-practices-bad-identifier.ga
gxformat2/examples/native/synthetic-unlinted-best-practices-dict-tool-state.ga
gxformat2/examples/native/synthetic-unlinted-best-practices.ga
gxformat2/mermaid/__init__.py
gxformat2/mermaid/_builder.py
gxformat2/mermaid/_cli.py
gxformat2/normalized/__init__.py
gxformat2/normalized/_conversion.py
gxformat2/normalized/_expanded.py
gxformat2/normalized/_format2.py
gxformat2/normalized/_native.py
gxformat2/normalized/_types.py
gxformat2/schema/__init__.py
gxformat2/schema/_input_parameter.py
gxformat2/schema/gxformat2.py
gxformat2/schema/gxformat2_strict.py
gxformat2/schema/json_schema.py
gxformat2/schema/native.py
gxformat2/schema/native_strict.py
gxformat2/schema/native_v0_1.py
gxformat2/schema/v19_09.py
tests/test_auto_label.py
tests/test_backward_compatiblitiy.py
tests/test_basic.py
tests/test_comments.py
tests/test_cytoscape.py
tests/test_cytoscape_layout.py
tests/test_cytoscape_layout_integration.py
tests/test_examples_catalog.py
tests/test_expand_inline_tool.py
tests/test_export_abstract.py
tests/test_inline_tool_helpers.py
tests/test_inline_tool_roundtrip.py
tests/test_interface_compat.py
tests/test_interop_tests.py
tests/test_lint.py
tests/test_lint_best_practices.py
tests/test_lint_planemo_compat.py
tests/test_lint_profiles.py
tests/test_linting.py
tests/test_load_native.py
tests/test_markdown_validate.py
tests/test_mermaid.py
tests/test_model_helpers.py
tests/test_native_schema.py
tests/test_normalize.py
tests/test_normalized.py
tests/test_post_job_action_import.py
tests/test_pydantic_schema.py
tests/test_resolve_source_reference.py
tests/test_schema.py
tests/test_schema_rules_catalog.py
tests/test_to_format2.py
tests/test_to_format2_model.py
tests/test_to_native.py
tests/test_to_native_model.py