Workflow Fixtures

Warning

These workflows are test fixtures, not examples of best-practice Galaxy workflows. They are designed to exercise specific code paths, edge cases, and linting checks. Many deliberately omit metadata, contain invalid references, or trigger warnings. Projects like Planemo can depend on these fixtures for shared test data.

Usage

from gxformat2.examples import get_path, load, load_contents, load_catalog

# Get file path
path = get_path("real-unicycler-assembly.ga")

# Load as parsed dict
workflow_dict = load("synthetic-basic.gxwf.yml")

# Load as raw string
yaml_str = load_contents("synthetic-basic.gxwf.yml")

# Load full catalog with pydantic models
for entry in load_catalog():
    print(entry.name, entry.origin, entry.workflow_label)

Naming Convention

Pattern: {origin}-{description}[-{variant}].{ext}

Origin prefix (required):

Prefix	Meaning
real	Exported from a real Galaxy instance, unmodified
real-hacked	Real workflow with manual edits (removed tools, added tags, etc.)
synthetic	Hand-written for testing purposes
converted	Machine-generated from another format

Description: kebab-case, descriptive. E.g. basic, nested-subworkflow, unicycler-assembly.

Variant (optional): appended with - for variations. E.g. -dict-tool-state, -bad-identifier.

Extension: .gxwf.yml for Format2 YAML, .ga for native Galaxy JSON.

Catalog

The authoritative catalog is gxformat2/examples/catalog.yml. Workflow metadata (label, annotation) is read from the workflow files themselves. A test validates that all catalog entries point to existing files and all example files appear in the catalog.

Each fixture’s test coverage is split into two categories:

• Python Tests — conventional pytest modules (tests/test_*.py)

• Interoperable Tests — YAML-driven declarative expectations (gxformat2/examples/expectations/*.yml) that are language-agnostic and can be reused from TypeScript or other implementations

Format2 Fixtures

synthetic-basic.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-basic.gxwf.yml

Workflow Label:

Simple workflow

Description:

Simple workflow that no-op cats a file and then selects 10 random lines.

Python Tests:

• tests/test_lint.py

• tests/test_basic.py

• tests/test_schema.py

• tests/test_to_native.py

• tests/test_export_abstract.py

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_ensure_format2_normalizes_format2 (ensure_format2)

• test_ensure_native_converts_format2 (ensure_native)

• test_bp_format2_clean (lint_best_practices_format2)

• test_bp_format2_no_creator (lint_best_practices_format2)

• test_bp_format2_no_license (lint_best_practices_format2)

• test_lint_basic_clean (lint_format2)

• test_basic_workflow_single_edge (workflow_to_mermaid_lines)

• test_input_type_alias_file (normalized_format2)

• test_outputs_dict_to_list (normalized_format2)

• test_to_native_basic_structure (to_native)

• test_to_native_input_step_type (to_native)

• test_to_native_tool_step (to_native)

• test_to_native_tool_connections (to_native)

• test_to_native_workflow_outputs (to_native)

• test_basic_valid_format2 (validate_format2)

• test_basic_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Simple workflow
doc: |
  Simple workflow that no-op cats a file and then selects 10 random lines.
inputs:
  the_input:
    type: File
    doc: input doc
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    doc: cat doc
    in:
      input1: the_input

synthetic-nested-subworkflow.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-nested-subworkflow.gxwf.yml

Description:

Workflow with an embedded subworkflow that runs random_lines inside a nested workflow step.

Python Tests:

• tests/test_lint.py

• tests/test_export_abstract.py

Interoperable Tests:

• test_lint_nested_subworkflow_clean (lint_format2)

• test_link_resolved_to_connected_value (normalized_format2)

• test_nested_subworkflow_valid_format2 (validate_format2)

• test_nested_subworkflow_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"outer_input<br/><i>data</i>"]
    step_0["first_cat"]
    step_1[["nested_workflow"]]
    step_2["split"]
    step_3["second_cat"]
    input_0 --> step_0
    step_0 --> step_1
    step_1 --> step_2
    step_2 --> step_3
    

Workflow source

class: GalaxyWorkflow
doc: |
  Workflow with an embedded subworkflow that runs random_lines inside a nested workflow step.
inputs:
  outer_input: data
outputs:
  outer_output:
    outputSource: second_cat/out_file1
steps:
  first_cat:
    tool_id: cat1
    in:
      input1: outer_input
  nested_workflow:
    run:
      class: GalaxyWorkflow
      inputs:
        inner_input: data
      outputs:
        workflow_output:
          outputSource: random_lines/out_file1
      steps:
        random_lines:
          tool_id: random_lines1
          state:
            num_lines: 2
            input:
              $link: inner_input
            seed_source:
              seed_source_selector: set_seed
              seed: asdf
    in:
      inner_input: first_cat/out_file1
  split:
    tool_id: split
    in:
      input1: nested_workflow/workflow_output
  second_cat:
    tool_id: cat_list
    in:
      input1: split/output

synthetic-unlinted-best-practices.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-unlinted-best-practices.gxwf.yml

Workflow Label:

bp (imported from uploaded file)

Python Tests:

• tests/test_lint_best_practices.py

Interoperable Tests:

• test_unlinted_best_practices_rejected_format2 (validate_format2)

• test_unlinted_best_practices_rejected_format2_strict (validate_format2_strict)

Workflow source

class: GalaxyWorkflow
label: bp (imported from uploaded file)
uuid: 66708ffe-c08c-4647-a7e9-fc7f731206a1
inputs:
  null:
    optional: false
    position:
      bottom: 730.3166656494141
      height: 82.55000305175781
      left: 1155
      right: 1355
      top: 647.7666625976562
      width: 200
      x: 1155
      y: 647.7666625976562
    type: data
outputs:
  _anonymous_output_1:
    outputSource: 1/outfile
steps:
  input:
    tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
    tool_version: 1.1.3
    position:
      bottom: 744.8333282470703
      height: 114.06666564941406
      left: 1465
      right: 1665
      top: 630.7666625976562
      width: 200
      x: 1465
      y: 630.7666625976562
    tool_state:
      infile:
        __class__: RuntimeValue
      replacements:
      - __index__: 0
        column: '1'
        find_pattern: ${report_name}
        replace_pattern: ''
    in: {}
    out:
      outfile:
        add_tags:
        - ${report_name}

synthetic-graph-simple.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-graph-simple.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_simple_graph_emits_two_nodes_one_edge (cytoscape_elements_to_list)

• test_simple_graph_input_node_shape (cytoscape_elements_to_list)

• test_simple_graph_tool_step_shape (cytoscape_elements_to_list)

• test_simple_graph_edge_shape (cytoscape_elements_to_list)

• test_simple_graph_header (workflow_to_mermaid_lines)

• test_simple_graph_data_input_shape (workflow_to_mermaid_lines)

• test_simple_graph_tool_step_shape (workflow_to_mermaid_lines)

• test_simple_graph_edge (workflow_to_mermaid_lines)

• test_simple_graph_exact (workflow_to_mermaid)

• test_simple_graph_extracts_main (normalized_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

format-version: v2.0
$graph:
  - id: main
    class: GalaxyWorkflow
    inputs:
      the_input: data
    outputs: {}
    steps:
      cat:
        tool_id: cat1
        in:
          input1: the_input

synthetic-graph-with-subworkflow.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-graph-with-subworkflow.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_subworkflow_step_classes (cytoscape_elements_to_list)

• test_subworkflow_edges (cytoscape_edge_ids)

• test_subworkflow_edge_named_output (cytoscape_elements_to_list)

• test_subworkflow_step_uses_double_bracket_shape (workflow_to_mermaid_lines)

• test_graph_inlines_subworkflow_ref (normalized_format2)

• test_to_native_inline_subworkflow (to_native)

Mermaid diagram

        graph LR
    input_0>"outer_input<br/><i>data</i>"]
    step_0["first_cat"]
    step_1[["nested_workflow"]]
    input_0 --> step_0
    step_0 --> step_1
    

Workflow source

format-version: v2.0
$graph:
  - id: subworkflow1
    class: GalaxyWorkflow
    inputs:
      inner_input: data
    outputs: {}
    steps:
      inner_tool:
        tool_id: random_lines1
        in:
          input: inner_input
  - id: main
    class: GalaxyWorkflow
    inputs:
      outer_input: data
    outputs: {}
    steps:
      first_cat:
        tool_id: cat1
        in:
          input1: outer_input
      nested_workflow:
        run: '#subworkflow1'
        in:
          inner_input: first_cat/out_file1

synthetic-inner-subworkflow.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-inner-subworkflow.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_inner_subworkflow_valid_format2 (validate_format2)

• test_inner_subworkflow_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"inner_input<br/><i>data</i>"]
    step_0["inner_tool"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  inner_input: data
outputs: {}
steps:
  inner_tool:
    tool_id: random_lines1
    in:
      input: inner_input

synthetic-input-shorthand.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-input-shorthand.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_input_shorthand_expanded (normalized_format2)

• test_no_tool_steps_format2 (normalized_format2)

• test_input_shorthand_valid_format2 (validate_format2)

• test_input_shorthand_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs: {}
steps: {}

synthetic-step-in-shorthand.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-step-in-shorthand.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_step_in_shorthand_expanded (normalized_format2)

• test_steps_without_run_unchanged (expanded_format2)

• test_null_tool_version (normalized_format2)

• test_step_in_shorthand_valid_format2 (validate_format2)

• test_step_in_shorthand_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0["s"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs: {}
steps:
  s:
    tool_id: cat1
    in:
      input1: x

synthetic-url-run-yml.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-url-run-yml.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_url_run_passes_through (normalized_format2)

• test_to_native_url_subworkflow (to_native)

• test_url_run_yml_valid_format2 (validate_format2)

• test_url_run_yml_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0[["nested"]]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs: {}
steps:
  nested:
    run: https://example.com/wf.yml
    in:
      x: x

synthetic-inner-nested-subworkflow.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-inner-nested-subworkflow.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_inner_nested_subworkflow_valid_format2 (validate_format2)

• test_inner_nested_subworkflow_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"y<br/><i>data</i>"]
    step_0[["inner_sub"]]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  y: data
outputs: {}
steps:
  inner_sub:
    run:
      class: GalaxyWorkflow
      inputs:
        inner_input: data
      outputs: {}
      steps:
        inner_tool:
          tool_id: random_lines1
          in:
            input: inner_input
    in:
      inner_input: y

synthetic-single-versioned-tool.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-single-versioned-tool.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_single_tool_format2 (normalized_format2)

• test_single_versioned_tool_valid_format2 (validate_format2)

• test_single_versioned_tool_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0["step1"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs: {}
steps:
  step1:
    tool_id: cat1
    tool_version: '1.0'
    in:
      x: x

synthetic-tool-with-inline-subworkflow.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-tool-with-inline-subworkflow.gxwf.yml

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_inline_subworkflow_format2 (normalized_format2)

• test_tool_with_inline_subworkflow_valid_format2 (validate_format2)

• test_tool_with_inline_subworkflow_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0["outer_tool"]
    step_1[["nested"]]
    input_0 --> step_0
    input_0 --> step_1
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs: {}
steps:
  outer_tool:
    tool_id: cat1
    tool_version: '1.0'
    in:
      x: x
  nested:
    type: subworkflow
    run:
      class: GalaxyWorkflow
      inputs:
        y: data
      outputs: {}
      steps:
        inner_tool:
          tool_id: sort1
          tool_version: '2.0'
          in:
            y: y
    in:
      y: x

synthetic-int-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-int-input.gxwf.yml

Interoperable Tests:

• test_int_input_step_type (cytoscape_node_ids)

• test_int_input_carries_int_step_type (cytoscape_elements_to_list)

• test_int_input_renders (workflow_to_mermaid_lines)

• test_to_native_int_input (to_native)

• test_int_input_valid_format2 (validate_format2)

• test_int_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_d<br/><i>data</i>"]
    input_1>"num_lines<br/><i>int</i>"]
    step_0["random_lines"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_d: File
  num_lines:
    type: int
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      num_lines: num_lines
      input: input_d
    state:
      seed_source:
        seed_source_selector: set_seed
        seed: asdf

synthetic-pause-step.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-pause-step.gxwf.yml

Interoperable Tests:

• test_to_native_pause_step (to_native)

• test_pause_step_valid_format2 (validate_format2)

• test_pause_step_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"test_input<br/><i>data</i>"]
    step_0["first_cat"]
    step_1["the_pause"]
    input_0 --> step_0
    step_0 --> step_1
    

Workflow source

class: GalaxyWorkflow
inputs:
  test_input: data
outputs: {}
steps:
  first_cat:
    tool_id: cat1
    in:
      input1: test_input
  the_pause:
    type: pause
    in:
      input: first_cat/out_file1

synthetic-comments-list.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-comments-list.gxwf.yml

Interoperable Tests:

• test_comments_list_preserved (normalized_format2)

• test_to_native_comments (to_native)

• test_comments_list_valid_format2 (validate_format2)

• test_comments_list_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  the_input: data
outputs: {}
steps: {}
comments:
  - type: text
    text: Hello world
    position: [10, 20]
    size: [100, 50]

synthetic-doc-array.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-doc-array.gxwf.yml

Description:

First line. Second line.

Interoperable Tests:

• test_doc_array_joined (normalized_format2)

• test_doc_array_valid_format2 (validate_format2)

• test_doc_array_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
doc:
  - "First line."
  - "Second line."
inputs:
  x: data
outputs: {}
steps: {}

synthetic-input-type-aliases.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-input-type-aliases.gxwf.yml

Interoperable Tests:

• test_input_type_alias_data_input (normalized_format2)

• test_input_type_aliases_valid_format2 (validate_format2)

• test_input_type_aliases_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"file_input<br/><i>data</i>"]
    input_1>"collection_input<br/><i>collection</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  file_input:
    type: data_input
  collection_input:
    type: data_collection
outputs: {}
steps: {}

synthetic-step-out-shorthand.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-step-out-shorthand.gxwf.yml

Interoperable Tests:

• test_step_out_shorthand_expanded (normalized_format2)

• test_step_out_shorthand_valid_format2 (validate_format2)

• test_step_out_shorthand_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0["step1"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs:
  final_output:
    outputSource: step1/out1
steps:
  step1:
    tool_id: cat1
    in:
      input1: x
    out:
      - out1

synthetic-inputs-array.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-inputs-array.gxwf.yml

Interoperable Tests:

• test_inputs_array_form (normalized_format2)

• test_inputs_array_valid_format2 (validate_format2)

• test_inputs_array_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  - id: x
    type: data
    label: "My Input"
outputs: {}
steps: {}

synthetic-tool-state-json.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-tool-state-json.gxwf.yml

Interoperable Tests:

• test_tool_state_json_parsed (normalized_format2)

• test_tool_state_json_valid_format2 (validate_format2)

• test_tool_state_json_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0["step1"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  x: data
outputs: {}
steps:
  step1:
    tool_id: cat1
    tool_state: '{"input1": "value1", "num_lines": 5}'
    in:
      input1: x

synthetic-tags.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-tags.gxwf.yml

Interoperable Tests:

• test_lint_tags_clean (lint_format2)

• test_tags_present (normalized_format2)

• test_tags_valid_format2 (validate_format2)

• test_tags_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
tags:
  - genomics
  - testing
inputs:
  x: data
outputs: {}
steps: {}

synthetic-optional-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-optional-input.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_optional_input_flag (normalized_format2)

• test_optional_input_valid_format2 (validate_format2)

• test_optional_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  the_input:
    type: File
    optional: true
outputs: {}
steps:
  cat:
    tool_id: cat_optional
    in:
      input1: the_input

synthetic-when-step.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-when-step.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_lint_when_step_clean (lint_format2)

• test_when_expression (normalized_format2)

• test_to_native_when_expression (to_native)

• test_when_step_valid_format2 (validate_format2)

• test_when_step_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_d<br/><i>data</i>"]
    input_1>"seed<br/><i>string</i>"]
    step_0["random_lines"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_d:
    type: data
  seed:
    type: string
    default: mycooldefault
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      'seed_source|seed': seed
      input: input_d
    state:
      num_lines: 5
      seed_source:
        seed_source_selector: set_seed
    when: $(inputs.seed != 'skip')

synthetic-pja-hide-rename.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-pja-hide-rename.gxwf.yml

Interoperable Tests:

• test_lint_pja_clean (lint_format2)

• test_pja_hide_and_rename (normalized_format2)

• test_to_native_pja_hide (to_native)

• test_to_native_pja_rename (to_native)

• test_pja_hide_rename_valid_format2 (validate_format2)

• test_pja_hide_rename_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input1<br/><i>data</i>"]
    step_0["first_cat"]
    step_1["second_cat"]
    input_0 --> step_0
    step_0 --> step_1
    

Workflow source

class: GalaxyWorkflow
inputs:
  input1: data
outputs:
  out1:
    outputSource: second_cat/out_file1
steps:
  first_cat:
    tool_id: cat1
    in:
      input1: input1
    out:
       out_file1:
         hide: true
         rename: "the new value"
  second_cat:
    tool_id: cat1
    in:
      input1: first_cat/out_file1

synthetic-paired-list-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-paired-list-input.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_paired_list_collection_type (normalized_format2)

• test_paired_list_input_valid_format2 (validate_format2)

• test_paired_list_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_list<br/><i>collection</i>"]
    step_0["random_lines"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_list:
    type: data_collection
    collection_type: list:paired
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      input: input_list
    state:
      num_lines: 5

synthetic-float-input-default.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-float-input-default.gxwf.yml

Interoperable Tests:

• test_lint_float_default_clean (lint_format2)

• test_float_type_and_default (normalized_format2)

• test_float_input_default_valid_format2 (validate_format2)

• test_float_input_default_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_d<br/><i>data</i>"]
    input_1{{"num_lines<br/><i>float</i>"}}
    step_0["random_lines"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_d: File
  num_lines:
    type: float
    default: 6.0
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      num_lines: num_lines
      input: input_d
    state:
      seed_source:
        seed_source_selector: set_seed
        seed: asdf

synthetic-string-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-string-input.gxwf.yml

Interoperable Tests:

• test_string_type_and_default (normalized_format2)

• test_pipe_separated_input_key (normalized_format2)

• test_string_input_valid_format2 (validate_format2)

• test_string_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_d<br/><i>data</i>"]
    input_1>"seed<br/><i>string</i>"]
    step_0["random_lines"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_d:
    type: data
  seed:
    type: string
    default: mycooldefault
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      'seed_source|seed': seed
      input: input_d
    state:
      num_lines: 5
      seed_source:
        seed_source_selector: set_seed

synthetic-integer-type-alias.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-integer-type-alias.gxwf.yml

Interoperable Tests:

• test_integer_type_alias (normalized_format2)

• test_integer_type_alias_valid_format2 (validate_format2)

• test_integer_type_alias_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_d<br/><i>data</i>"]
    input_1{{"num_lines<br/><i>integer</i>"}}
    step_0["random_lines"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_d:
    type: data
  num_lines:
    type: integer
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      num_lines: num_lines
      input: input_d
    state:
      seed_source:
        seed_source_selector: set_seed
        seed: asdf

synthetic-multi-data-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-multi-data-input.gxwf.yml

Workflow Label:

Multi-data input

Python Tests:

• tests/test_basic.py

• tests/test_to_native.py

Interoperable Tests:

• test_multi_data_inputs_distinct_ids (cytoscape_node_ids)

• test_multi_data_inputs_two_edges (cytoscape_edge_ids)

• test_multi_data_inputs_distinct_ids (workflow_to_mermaid_lines)

• test_multi_data_input_sources (normalized_format2)

• test_to_native_multi_data_connections (to_native)

• test_multi_data_input_valid_format2 (validate_format2)

• test_multi_data_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"optional<br/><i>data</i>"]
    input_1>"required<br/><i>data</i>"]
    step_0["count_multi_file"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Multi-data input
inputs:
  optional:
    optional: true
    type: data
  required:
    optional: false
    type: data
outputs: {}
steps:
  count_multi_file:
    tool_id: count_multi_file
    in:
      input1:
        source:
        - required
        - optional

synthetic-multi-string-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-multi-string-input.gxwf.yml

Workflow Label:

Multi-string input

Python Tests:

• tests/test_to_native.py

Interoperable Tests:

• test_multi_string_input_type (normalized_format2)

• test_multi_string_input_valid_format2 (validate_format2)

• test_multi_string_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"multi-text<br/><i>string</i>"]
    

Workflow source

class: GalaxyWorkflow
label: Multi-string input
inputs:
  multi-text:
    optional: false
    type: [string]
outputs: {}
steps: []

synthetic-rules-tool.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-rules-tool.gxwf.yml

Interoperable Tests:

• test_lint_rules_tool_clean (lint_format2)

• test_rules_tool_link_resolution (normalized_format2)

• test_rules_tool_valid_format2 (validate_format2)

• test_rules_tool_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_c<br/><i>collection</i>"]
    step_0["apply"]
    step_1["random_lines"]
    input_0 --> step_0
    step_0 --> step_1
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_c: collection
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  apply:
    tool_id: __APPLY_RULES__
    state:
      input:
        $link: input_c
      rules:
        rules:
          - type: add_column_metadata
            value: identifier0
          - type: add_column_metadata
            value: identifier0
        mapping:
          - type: list_identifiers
            columns: [0, 1]
  random_lines:
    tool_id: random_lines1
    state:
      num_lines: 1
      input:
        $link: apply/output
      seed_source:
        seed_source_selector: set_seed
        seed: asdf

synthetic-runtime-inputs.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-runtime-inputs.gxwf.yml

Python Tests:

• tests/test_to_native.py

Interoperable Tests:

• test_lint_runtime_inputs_clean (lint_format2)

• test_runtime_inputs (normalized_format2)

• test_runtime_inputs_valid_format2 (validate_format2)

• test_runtime_inputs_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input1<br/><i>data</i>"]
    step_0["the_pause"]
    step_1["random"]
    input_0 --> step_0
    step_0 --> step_1
    

Workflow source

class: GalaxyWorkflow
inputs:
  input1: data
outputs:
  out1:
    outputSource: random/out_file1
steps:
  the_pause:
    type: pause
    in:
      input: input1
  random:
    tool_id: random_lines1
    runtime_inputs:
      - num_lines
    state:
      input:
        $link: the_pause
      seed_source:
        seed_source_selector: set_seed
        seed: asdf

synthetic-slash-in-input-label.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-slash-in-input-label.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_slash_in_input_label_normalized (normalized_format2)

• test_slash_in_input_label_to_native (to_native)

• test_slash_in_input_label_valid_format2 (validate_format2)

• test_slash_in_input_label_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"Host/Contaminant Genome<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  Host/Contaminant Genome: data
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: Host/Contaminant Genome

synthetic-slash-in-step-label.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-slash-in-step-label.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_slash_in_step_label_normalized (normalized_format2)

• test_slash_in_step_label_valid_format2 (validate_format2)

• test_slash_in_step_label_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["Host/Contaminant Filter"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  the_input: data
outputs:
  the_output:
    outputSource: Host/Contaminant Filter/out_file1
steps:
  Host/Contaminant Filter:
    tool_id: cat1
    in:
      input1: the_input

synthetic-slash-in-label-chained.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-slash-in-label-chained.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_lint_slash_labels_clean (lint_format2)

• test_slash_in_label_chained_connection (normalized_format2)

• test_slash_in_label_chained_to_native (to_native)

• test_slash_in_label_chained_valid_format2 (validate_format2)

• test_slash_in_label_chained_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"Host/Contaminant Genome<br/><i>data</i>"]
    step_0["Host/Contaminant Filter"]
    step_1["second_cat"]
    input_0 --> step_0
    step_0 --> step_1
    

Workflow source

class: GalaxyWorkflow
inputs:
  Host/Contaminant Genome: data
outputs:
  the_output:
    outputSource: second_cat/out_file1
steps:
  Host/Contaminant Filter:
    tool_id: cat1
    in:
      input1: Host/Contaminant Genome
  second_cat:
    tool_id: cat1
    in:
      input1: Host/Contaminant Filter/out_file1

synthetic-sample-sheet-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-sample-sheet-input.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_sample_sheet_collection_type (normalized_format2)

• test_sample_sheet_input_valid_format2 (validate_format2)

• test_sample_sheet_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_sample_sheet<br/><i>collection</i>"]
    step_0["random_lines"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_sample_sheet:
    type: data_collection
    collection_type: sample_sheet
    column_definitions:
    - type: string
      restrictions:
        - treatment
        - control
      name: condition
      default_value: treatment
      optional: false
outputs:
  out1:
    outputSource: random_lines/out_file1
steps:
  random_lines:
    tool_id: random_lines1
    in:
      input: input_sample_sheet
    state:
      num_lines: 5

synthetic-text-restrictions.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-text-restrictions.gxwf.yml

Interoperable Tests:

• test_text_restrictions_valid_format2 (validate_format2)

• test_text_restrictions_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0{{"treatment<br/><i>text</i>"}}
    

Workflow source

class: GalaxyWorkflow
inputs:
  treatment:
    type: text
    restrictions:
      - control
      - treatment
outputs: {}
steps: {}

synthetic-text-restrictions-options.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-text-restrictions-options.gxwf.yml

Interoperable Tests:

• test_text_restrictions_options_valid_format2 (validate_format2)

• test_text_restrictions_options_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0{{"treatment<br/><i>text</i>"}}
    

Workflow source

class: GalaxyWorkflow
inputs:
  treatment:
    type: text
    restrictions:
      - {value: control, label: Control}
      - {value: treatment, label: Treatment}
outputs: {}
steps: {}

synthetic-text-suggestions.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-text-suggestions.gxwf.yml

Interoperable Tests:

• test_text_suggestions_valid_format2 (validate_format2)

• test_text_suggestions_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0{{"hint<br/><i>text</i>"}}
    

Workflow source

class: GalaxyWorkflow
inputs:
  hint:
    type: text
    suggestions:
      - alpha
      - {value: beta, label: Beta}
outputs: {}
steps: {}

synthetic-text-restrict-on-connections.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-text-restrict-on-connections.gxwf.yml

Interoperable Tests:

• test_text_restrict_on_connections_valid_format2 (validate_format2)

• test_text_restrict_on_connections_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0{{"select_text<br/><i>text</i>"}}
    

Workflow source

class: GalaxyWorkflow
inputs:
  select_text:
    type: text
    restrictOnConnections: true
outputs: {}
steps: {}

synthetic-bad-restrictions-on-data.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bad-restrictions-on-data.gxwf.yml

Interoperable Tests:

• test_restrictions_on_data_rejected_format2 (validate_format2)

• test_restrictions_on_data_rejected_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"bad<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  bad:
    type: data
    restrictions:
      - x
outputs: {}
steps: {}

synthetic-bad-column-defs-on-list.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bad-column-defs-on-list.gxwf.yml

Interoperable Tests:

• test_column_defs_on_list_rejected_format2 (validate_format2)

• test_column_defs_on_list_rejected_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"bad<br/><i>collection</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  bad:
    type: collection
    collection_type: list
    column_definitions:
      - name: cond
        type: string
        optional: false
outputs: {}
steps: {}

synthetic-bad-column-default-mismatch.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bad-column-default-mismatch.gxwf.yml

Interoperable Tests:

• test_column_default_mismatch_rejected_format2 (validate_format2)

• test_column_default_mismatch_rejected_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"ss<br/><i>collection</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  ss:
    type: collection
    collection_type: sample_sheet
    column_definitions:
      - name: replicate
        type: int
        optional: false
        default_value: not_an_int
outputs: {}
steps: {}

synthetic-record-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-record-input.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_record_collection_type_and_fields (normalized_format2)

• test_record_fields_round_trip_to_native (to_native)

• test_record_input_valid_format2 (validate_format2)

• test_record_input_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"input_record<br/><i>collection</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  input_record:
    type: collection
    collection_type: record
    fields:
      - name: parent
        type: File
      - name: child
        type:
          - File
          - "null"
outputs: {}
steps: {}

synthetic-bad-fields-on-list.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bad-fields-on-list.gxwf.yml

Interoperable Tests:

• test_fields_on_list_rejected_format2 (validate_format2)

• test_fields_on_list_rejected_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"bad<br/><i>collection</i>"]
    

Workflow source

class: GalaxyWorkflow
inputs:
  bad:
    type: collection
    collection_type: list
    fields:
      - name: parent
        type: File
outputs: {}
steps: {}

synthetic-comments-dict.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-comments-dict.gxwf.yml

Python Tests:

• tests/test_comments.py

Interoperable Tests:

• test_frame_comments_ignored_by_default (workflow_to_mermaid)

• test_frame_comments_not_emitted_without_flag (workflow_to_mermaid)

• test_frame_comments_rendered_as_subgraph (workflow_to_mermaid_with_comments_lines)

• test_comments_dict_to_list (normalized_format2)

• test_to_native_comments_dict (to_native)

• test_comments_dict_valid_format2 (validate_format2)

• test_comments_dict_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    subgraph sub_0 ["Preprocessing"]
        step_0["cat"]
    end
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  the_input: data
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input
comments:
  adapter_warning:
    type: text
    position: [100, 200]
    size: [200, 50]
    color: blue
    text: "Check adapters"
    text_size: 2
    bold: true

  preprocessing_docs:
    type: markdown
    position: [300, 50]
    size: [400, 300]
    text: |
      # Preprocessing Pipeline
      Quality filtering and adapter trimming.

  preprocessing:
    type: frame
    position: [50, 50]
    size: [600, 400]
    color: green
    title: Preprocessing
    contains_steps:
      - cat
    contains_comments:
      - adapter_warning
      - preprocessing_docs

synthetic-user-defined-tool.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-user-defined-tool.gxwf.yml

Python Tests:

• tests/test_basic.py

Interoperable Tests:

• test_lint_user_defined_tool_clean (lint_format2)

• test_user_defined_tool_run (normalized_format2)

• test_to_native_user_defined_tool (to_native)

• test_user_defined_tool_valid_format2 (validate_format2)

• test_user_defined_tool_valid_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["my_tool"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  the_input: data
outputs:
  the_output:
    outputSource: my_tool/output1
steps:
  my_tool:
    run:
      class: GalaxyUserTool
      id: cat_user_defined
      version: "0.1"
      name: cat_user_defined
      description: concatenates a file
      container: busybox
      shell_command: cat '$(inputs.input1.path)' > output.txt
      inputs:
        - name: input1
          type: data
          format: txt
      outputs:
        - name: output1
          type: data
          format: txt
          from_work_dir: output.txt
    in:
      input1: the_input

synthetic-extra-field.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-extra-field.gxwf.yml

Workflow Label:

Extra field workflow

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_extra_field_valid_format2_lax (validate_format2)

• test_extra_field_rejected_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Extra field workflow
not_a_real_field: should cause strict validation failure
inputs:
  x:
    type: File
outputs: {}
steps:
  cat:
    tool_id: cat1
    in:
      input1: x

synthetic-missing-steps.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-missing-steps.gxwf.yml

Workflow Label:

Missing steps

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_lint_format2_missing_steps (lint_format2)

• test_missing_steps_rejected_format2 (validate_format2)

• test_missing_steps_rejected_format2_strict (validate_format2_strict)

Mermaid diagram

        graph LR
    input_0>"x<br/><i>data</i>"]
    

Workflow source

class: GalaxyWorkflow
label: Missing steps
inputs:
  x:
    type: File

synthetic-lint-no-class.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-no-class.gxwf.yml

Interoperable Tests:

• test_lint_format2_missing_class (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input

synthetic-lint-nested-no-steps.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-nested-no-steps.gxwf.yml

Workflow Label:

Nested subworkflow missing steps

Interoperable Tests:

• test_lint_format2_nested_no_steps (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0[["subwf"]]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Nested subworkflow missing steps
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: subwf/out
steps:
  subwf:
    run:
      class: GalaxyWorkflow
      inputs:
        inner_input:
          type: File
      outputs:
        out:
          outputSource: missing/out_file1
    in:
      inner_input: the_input

synthetic-lint-step-errors.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-step-errors.gxwf.yml

Workflow Label:

Step with errors

Interoperable Tests:

• test_lint_format2_step_errors (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Step with errors
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    errors: "Tool is not installed"
    in:
      input1: the_input

synthetic-lint-testtoolshed.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-testtoolshed.gxwf.yml

Workflow Label:

TestToolShed reference

Interoperable Tests:

• test_lint_format2_testtoolshed (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: TestToolShed reference
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: testtoolshed.g2.bx.psu.edu/repos/devteam/cat/cat1/1.0.0
    in:
      input1: the_input

synthetic-lint-bad-output-source.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-bad-output-source.gxwf.yml

Workflow Label:

Bad output source

Interoperable Tests:

• test_lint_format2_bad_output_source (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Bad output source
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: nonexistent_step/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input

synthetic-lint-bad-int-default.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-bad-int-default.gxwf.yml

Workflow Label:

Bad int default

Interoperable Tests:

• test_lint_format2_bad_int_default (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>int</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Bad int default
inputs:
  the_input:
    type: int
    default: "not_an_int"
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input

synthetic-lint-bad-float-default.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-bad-float-default.gxwf.yml

Workflow Label:

Bad float default

Interoperable Tests:

• test_lint_format2_bad_float_default (lint_format2)

Mermaid diagram

        graph LR
    input_0{{"the_input<br/><i>float</i>"}}
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Bad float default
inputs:
  the_input:
    type: float
    default: "not_a_float"
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input

synthetic-lint-bad-string-default.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-bad-string-default.gxwf.yml

Workflow Label:

Bad string default

Interoperable Tests:

• test_lint_format2_bad_string_default (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>string</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Bad string default
inputs:
  the_input:
    type: string
    default: 42
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input

synthetic-lint-report.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-report.gxwf.yml

Workflow Label:

Workflow with report

Interoperable Tests:

• test_lint_format2_report_clean (lint_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Workflow with report
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input
report:
  markdown: |
    # Workflow Report
    Some text.

synthetic-lint-report-bad-type.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-lint-report-bad-type.gxwf.yml

Workflow Label:

Report with bad markdown type

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_report_bad_type_rejected_format2 (validate_format2)

• test_report_bad_type_rejected_format2_strict (validate_format2_strict)

Workflow source

class: GalaxyWorkflow
label: Report with bad markdown type
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    in:
      input1: the_input
report:
  markdown: 42

synthetic-bp-no-annotation.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bp-no-annotation.gxwf.yml

Workflow Label:

No annotation workflow

Interoperable Tests:

• test_bp_format2_no_annotation (lint_best_practices_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: No annotation workflow
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    doc: cat doc
    in:
      input1: the_input

synthetic-bp-disconnected-input.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bp-disconnected-input.gxwf.yml

Workflow Label:

Disconnected input workflow

Description:

A workflow with a disconnected step input.

Interoperable Tests:

• test_bp_format2_disconnected_input (lint_best_practices_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Disconnected input workflow
doc: A workflow with a disconnected step input.
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: cat/out_file1
steps:
  cat:
    tool_id: cat1
    doc: cat doc
    in:
      input1: the_input
      disconnected_input: {}

synthetic-bp-step-no-label.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-bp-step-no-label.gxwf.yml

Workflow Label:

Step without label

Description:

A workflow where steps use list form without labels.

Interoperable Tests:

• test_bp_format2_step_no_label (lint_best_practices_format2)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["1"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
label: Step without label
doc: A workflow where steps use list form without labels.
inputs:
  the_input:
    type: File
outputs:
  the_output:
    outputSource: 0/out_file1
steps:
  - tool_id: cat1
    doc: cat doc
    in:
      input1: the_input

synthetic-int-link.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-int-link.gxwf.yml

Description:

``$link`` value parsed by YAML as an integer (e.g. ``$link: 0``). The resolver expects a string source reference, so unquoted-numeric values are coerced before source resolution.

Interoperable Tests:

• test_int_link_coerced_to_str (normalized_format2)

Mermaid diagram

        graph LR
    input_0>"myinput<br/><i>data</i>"]
    step_0["cat"]
    

Workflow source

class: GalaxyWorkflow
doc: |
  ``$link`` value parsed by YAML as an integer (e.g. ``$link: 0``). The
  resolver expects a string source reference, so unquoted-numeric values
  are coerced before source resolution.
inputs:
  myinput: data
steps:
  cat:
    tool_id: cat1
    state:
      input1:
        $link: 0

synthetic-multisource-bare-list.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-multisource-bare-list.gxwf.yml

Description:

Dict-form ``in:`` value as a bare YAML list of source references for a multi-source input. The schema’s ``mapPredicate: source`` shorthand permits this and ``Sink.source`` accepts ``list[str]``.

Interoperable Tests:

• test_multisource_bare_list (normalized_format2)

Mermaid diagram

        graph LR
    input_0>"input1<br/><i>data</i>"]
    input_1>"input2<br/><i>data</i>"]
    step_0["count_multi_file"]
    input_0 --> step_0
    input_1 --> step_0
    

Workflow source

class: GalaxyWorkflow
doc: |
  Dict-form ``in:`` value as a bare YAML list of source references for a
  multi-source input. The schema's ``mapPredicate: source`` shorthand
  permits this and ``Sink.source`` accepts ``list[str]``.
inputs:
  input1: data
  input2: data
steps:
  count_multi_file:
    tool_id: count_multi_file
    in:
      input1:
        - input1
        - input2

synthetic-step-post-job-actions.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-step-post-job-actions.gxwf.yml

Description:

Step-level explicit ``post_job_actions:`` map. Cribbed from Galaxy’s ``test_validated_post_job_action_validated`` to exercise PJAs that have no ``out:`` shorthand (``ValidateOutputsAction`` operates on the step as a whole, not on a specific output). See gxformat2 #206.

Interoperable Tests:

• test_step_post_job_actions_normalized (normalized_format2)

• test_step_post_job_actions_to_native (to_native)

• test_step_post_job_actions_round_trip (ensure_native)

Mermaid diagram

        graph LR
    input_0>"input1<br/><i>data</i>"]
    step_0["first_cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
doc: |
  Step-level explicit ``post_job_actions:`` map.  Cribbed from Galaxy's
  ``test_validated_post_job_action_validated`` to exercise PJAs that have
  no ``out:`` shorthand (``ValidateOutputsAction`` operates on the step
  as a whole, not on a specific output).  See gxformat2 #206.
inputs:
  input1: data
outputs:
  wf_output_1:
    outputSource: first_cat/out_file1
steps:
  first_cat:
    tool_id: cat1
    in:
      input1: input1
    post_job_actions:
      ValidateOutputsAction:
        action_type: ValidateOutputsAction

synthetic-step-post-job-actions-merged.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-step-post-job-actions-merged.gxwf.yml

Description:

Step has both an ``out:`` shorthand PJA (``rename:``) and an explicit ``post_job_actions:`` entry — both should appear in the native step.

Interoperable Tests:

• test_step_post_job_actions_merged_with_out_shorthand (to_native)

Mermaid diagram

        graph LR
    input_0>"input1<br/><i>data</i>"]
    step_0["first_cat"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
doc: |
  Step has both an ``out:`` shorthand PJA (``rename:``) and an explicit
  ``post_job_actions:`` entry — both should appear in the native step.
inputs:
  input1: data
steps:
  first_cat:
    tool_id: cat1
    in:
      input1: input1
    out:
      out_file1:
        rename: renamed.txt
    post_job_actions:
      ValidateOutputsAction:
        action_type: ValidateOutputsAction

synthetic-step-input-default-scalar.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-step-input-default-scalar.gxwf.yml

Interoperable Tests:

• test_to_native_step_input_default_scalar (to_native)

Mermaid diagram

        graph LR
    input_0>"inner_input<br/><i>data</i>"]
    step_0["random_lines"]
    input_0 --> step_0
    

Workflow source

class: GalaxyWorkflow
inputs:
  inner_input: data
steps:
  random_lines:
    tool_id: random_lines1
    in:
      input: inner_input
      num_lines:
        default: 2
      seed_source|seed_source_selector:
        default: set_seed
      seed_source|seed:
        default: asdf

synthetic-step-input-default-file.gxwf.yml

Origin:

synthetic

Format:

format2

Path:

format2/synthetic-step-input-default-file.gxwf.yml

Interoperable Tests:

• test_to_native_step_input_default_file (to_native)

Mermaid diagram

        graph LR
    step_0["cat1"]
    

Workflow source

class: GalaxyWorkflow
steps:
  cat1:
    tool_id: cat1
    in:
      input1:
        default:
          class: File
          basename: a file
          format: txt
          location: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed

Native Fixtures

real-unicycler-assembly.ga

Origin:

real

Format:

native

Path:

native/real-unicycler-assembly.ga

Workflow Label:

Unicycler training

Description:

Unicycler genome assembly workflow from Galaxy Training Materials.

Python Tests:

• tests/test_lint.py

• tests/test_basic.py

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_lint_native_unicycler_clean (lint_native)

• test_unicycler_assembly_valid_native (validate_native)

• test_unicycler_assembly_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"Forward reads<br/><i>data</i>"]
    input_1>"Reverse Reads<br/><i>data</i>"]
    input_2>"Long Reads<br/><i>data</i>"]
    step_0["tool:devteam/fastqc/fastqc/0.71"]
    step_1["tool:devteam/fastqc/fastqc/0.71"]
    step_2["tool:iuc/unicycler/unicycler/0.2.0"]
    step_3["tool:iuc/quast/quast/4.1.1"]
    step_4["tool:crs4/prokka/prokka/1.12.0"]
    input_0 --> step_0
    input_1 --> step_1
    input_1 --> step_2
    input_0 --> step_2
    input_2 --> step_2
    step_2 --> step_3
    step_2 --> step_4
    

Workflow source

{
  "uuid": "2fa1768f-116d-4695-83c5-6a07eff7be33",
  "tags": [],
  "format-version": "0.1",
  "name": "Unicycler training",
  "steps": {
    "0": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"forward_reads\"}",
      "id": 0,
      "uuid": "1e8ef78c-1cb2-4376-9fc5-3f9d47acfe69",
      "errors": null,
      "name": "Input dataset",
      "label": "Forward reads",
      "inputs": [
        {
          "name": "forward_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 346,
        "left": 160.98333740234375
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "1": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"reverse_reads\"}",
      "id": 1,
      "uuid": "251d7a96-2b0d-4b8c-bf34-d24b65b32b41",
      "errors": null,
      "name": "Input dataset",
      "label": "Reverse Reads",
      "inputs": [
        {
          "name": "reverse_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 683,
        "left": 103.9666748046875
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "2": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"long_reads\"}",
      "id": 2,
      "uuid": "80a96186-0c6f-448e-a8cd-11f18e04629d",
      "errors": null,
      "name": "Input dataset",
      "label": "Long Reads",
      "inputs": [
        {
          "name": "long_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 878.9833374023438,
        "left": 103
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "3": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "tool_version": "0.71",
      "outputs": [
        {
          "type": "html",
          "name": "html_file"
        },
        {
          "type": "txt",
          "name": "text_file"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "input_file": {
          "output_name": "output",
          "id": 0
        }
      },
      "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 3,
      "tool_shed_repository": {
        "owner": "devteam",
        "changeset_revision": "ff9530579d1f",
        "name": "fastqc",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "ca4cf888-bf14-4cc9-9bc1-202b3ed818d0",
      "errors": null,
      "name": "FastQC",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "contaminants",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "limits",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "input_file",
          "description": "runtime parameter for tool FastQC"
        }
      ],
      "position": {
        "top": 271.31666564941406,
        "left": 684.8333129882812
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "type": "tool"
    },
    "4": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "tool_version": "0.71",
      "outputs": [
        {
          "type": "html",
          "name": "html_file"
        },
        {
          "type": "txt",
          "name": "text_file"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "input_file": {
          "output_name": "output",
          "id": 1
        }
      },
      "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 4,
      "tool_shed_repository": {
        "owner": "devteam",
        "changeset_revision": "ff9530579d1f",
        "name": "fastqc",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "988ebf23-99af-4b76-a476-28b58f505f61",
      "errors": null,
      "name": "FastQC",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "contaminants",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "limits",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "input_file",
          "description": "runtime parameter for tool FastQC"
        }
      ],
      "position": {
        "top": 603,
        "left": 339.98333740234375
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "type": "tool"
    },
    "5": {
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real-hacked-unicycler-assembly-with-tags.ga

Origin:

real-hacked

Format:

native

Path:

native/real-hacked-unicycler-assembly-with-tags.ga

Workflow Label:

Unicycler training

Description:

Unicycler workflow

Python Tests:

• tests/test_lint.py

Interoperable Tests:

• test_unicycler_assembly_with_tags_valid_native (validate_native)

• test_unicycler_assembly_with_tags_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"Forward reads<br/><i>data</i>"]
    input_1>"Reverse Reads<br/><i>data</i>"]
    input_2>"Long Reads<br/><i>data</i>"]
    step_0["tool:devteam/fastqc/fastqc/0.71"]
    step_1["tool:devteam/fastqc/fastqc/0.71"]
    step_2["tool:iuc/unicycler/unicycler/0.2.0"]
    step_3["tool:iuc/quast/quast/4.1.1"]
    step_4["tool:crs4/prokka/prokka/1.12.0"]
    input_0 --> step_0
    input_1 --> step_1
    input_1 --> step_2
    input_0 --> step_2
    input_2 --> step_2
    step_2 --> step_3
    step_2 --> step_4
    

Workflow source

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      "errors": null,
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      "label": "Reverse Reads",
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      "name": "Input dataset",
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          "name": "out_fna"
        },
        {
          "type": "fasta",
          "name": "out_faa"
        },
        {
          "type": "fasta",
          "name": "out_ffn"
        },
        {
          "type": "asn1",
          "name": "out_sqn"
        },
        {
          "type": "fasta",
          "name": "out_fsa"
        },
        {
          "type": "txt",
          "name": "out_tbl"
        },
        {
          "type": "txt",
          "name": "out_err"
        },
        {
          "type": "txt",
          "name": "out_txt"
        },
        {
          "type": "txt",
          "name": "out_log"
        }
      ],
      "workflow_outputs": [
        {
          "output_name": "out_ffn",
          "label": "ffn"
        },
        {
          "output_name": "out_gbk",
          "label": "gbk"
        },
        {
          "output_name": "out_tbl",
          "label": "tbl"
        }
      ],
      "input_connections": {
        "input": {
          "output_name": "assembly",
          "id": 5
        }
      },
      "tool_state": "{\"strain\": \"\\\"C\\\"\", \"increment\": \"\\\"10\\\"\", \"species\": \"\\\"Coli\\\"\", \"__page__\": null, \"usegenus\": \"\\\"true\\\"\", \"evalue\": \"\\\"1e-06\\\"\", \"compliant\": \"{\\\"mincontig\\\": \\\"200\\\", \\\"__current_case__\\\": 0, \\\"compliant_select\\\": \\\"no\\\", \\\"addgenes\\\": \\\"false\\\"}\", \"fast\": \"\\\"false\\\"\", \"__job_resource\": \"{\\\"__current_case__\\\": 0, \\\"__job_resource__select\\\": \\\"no\\\"}\", \"locustag\": \"\\\"PROKKA\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"kingdom\": \"{\\\"gcode\\\": \\\"11\\\", \\\"kingdom_select\\\": \\\"Bacteria\\\", \\\"__current_case__\\\": 1}\", \"metagenome\": \"\\\"false\\\"\", \"centre\": \"\\\"\\\"\", \"outputs\": \"[\\\"gff\\\", \\\"gbk\\\", \\\"fna\\\", \\\"faa\\\", \\\"ffn\\\", \\\"sqn\\\", \\\"fsa\\\", \\\"tbl\\\", \\\"err\\\", \\\"txt\\\"]\", \"gffver\": \"\\\"3\\\"\", \"norrna\": \"\\\"false\\\"\", \"proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"notrna\": \"\\\"false\\\"\", \"plasmid\": \"\\\"\\\"\", \"rfam\": \"\\\"false\\\"\", \"genus\": \"\\\"Escherichia\\\"\", \"chromInfo\": \"\\\"/galaxy-repl/localdata/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
      "id": 7,
      "tool_shed_repository": {
        "owner": "crs4",
        "changeset_revision": "a17498c603ec",
        "name": "prokka",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "9a6e8f35-351c-42c4-bbe0-9a9da64ae1a8",
      "errors": null,
      "name": "Prokka",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "input",
          "description": "runtime parameter for tool Prokka"
        },
        {
          "name": "proteins",
          "description": "runtime parameter for tool Prokka"
        }
      ],
      "position": {
        "top": 555,
        "left": 1100.9833984375
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0",
      "type": "tool"
    }
  },
  "annotation": "Unicycler workflow",
  "a_galaxy_workflow": "true"
}

real-hacked-unicycler-assembly-no-tool.ga

Origin:

real-hacked

Format:

native

Path:

native/real-hacked-unicycler-assembly-no-tool.ga

Workflow Label:

Unicycler training

Description:

Unicycler with one tool deliberately removed to test missing-tool linting.

Python Tests:

• tests/test_lint.py

Interoperable Tests:

• test_lint_native_missing_tool_warns (lint_native)

• test_unicycler_assembly_no_tool_valid_native (validate_native)

• test_unicycler_assembly_no_tool_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"Forward reads<br/><i>data</i>"]
    input_1>"Reverse Reads<br/><i>data</i>"]
    input_2>"Long Reads<br/><i>data</i>"]
    step_0["tool:devteam/fastqc/fastqc/0.71"]
    step_1["tool:devteam/fastqc/fastqc/0.71"]
    step_2["tool:iuc/unicycler/unicycler/0.2.0"]
    step_3["tool:iuc/quast/quast/4.1.1"]
    step_4["tool:crs4/prokka/prokka/1.12.0"]
    input_0 --> step_0
    input_1 --> step_1
    input_1 --> step_2
    input_0 --> step_2
    input_2 --> step_2
    step_2 --> step_3
    step_2 --> step_4
    

Workflow source

{
  "uuid": "2fa1768f-116d-4695-83c5-6a07eff7be33",
  "tags": [],
  "format-version": "0.1",
  "name": "Unicycler training",
  "steps": {
    "0": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"forward_reads\"}",
      "id": 0,
      "uuid": "1e8ef78c-1cb2-4376-9fc5-3f9d47acfe69",
      "errors": null,
      "name": "Input dataset",
      "label": "Forward reads",
      "inputs": [
        {
          "name": "forward_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 346,
        "left": 160.98333740234375
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "1": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"reverse_reads\"}",
      "id": 1,
      "uuid": "251d7a96-2b0d-4b8c-bf34-d24b65b32b41",
      "errors": null,
      "name": "Input dataset",
      "label": "Reverse Reads",
      "inputs": [
        {
          "name": "reverse_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 683,
        "left": 103.9666748046875
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "2": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"long_reads\"}",
      "id": 2,
      "uuid": "80a96186-0c6f-448e-a8cd-11f18e04629d",
      "errors": null,
      "name": "Input dataset",
      "label": "Long Reads",
      "inputs": [
        {
          "name": "long_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 878.9833374023438,
        "left": 103
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "3": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "tool_version": "0.71",
      "outputs": [
        {
          "type": "html",
          "name": "html_file"
        },
        {
          "type": "txt",
          "name": "text_file"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "input_file": {
          "output_name": "output",
          "id": 0
        }
      },
      "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 3,
      "tool_shed_repository": {
        "owner": "devteam",
        "changeset_revision": "ff9530579d1f",
        "name": "fastqc",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "ca4cf888-bf14-4cc9-9bc1-202b3ed818d0",
      "errors": null,
      "name": "FastQC",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "contaminants",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "limits",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "input_file",
          "description": "runtime parameter for tool FastQC"
        }
      ],
      "position": {
        "top": 271.31666564941406,
        "left": 684.8333129882812
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "type": "tool"
    },
    "4": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "tool_version": "0.71",
      "outputs": [
        {
          "type": "html",
          "name": "html_file"
        },
        {
          "type": "txt",
          "name": "text_file"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "input_file": {
          "output_name": "output",
          "id": 1
        }
      },
      "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 4,
      "tool_shed_repository": {
        "owner": "devteam",
        "changeset_revision": "ff9530579d1f",
        "name": "fastqc",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "988ebf23-99af-4b76-a476-28b58f505f61",
      "errors": null,
      "name": "FastQC",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "contaminants",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "limits",
          "description": "runtime parameter for tool FastQC"
        },
        {
          "name": "input_file",
          "description": "runtime parameter for tool FastQC"
        }
      ],
      "position": {
        "top": 603,
        "left": 339.98333740234375
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
      "type": "tool"
    },
    "5": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0",
      "tool_version": "0.2.0",
      "outputs": [
        {
          "type": "txt",
          "name": "assembly_grapth"
        },
        {
          "type": "fasta",
          "name": "assembly"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "paired_unpaired|fastq_input2": {
          "output_name": "output",
          "id": 1
        },
        "paired_unpaired|fastq_input1": {
          "output_name": "output",
          "id": 0
        },
        "long_reads": {
          "output_name": "output",
          "id": 2
        }
      },
      "tool_state": "{\"__page__\": null, \"spades\": \"{\\\"min_kmer_frac\\\": \\\"\\\", \\\"max_kmer_frac\\\": \\\"\\\", \\\"kmer_count\\\": \\\"\\\"}\", \"graph_clean\": \"{\\\"min_dead_end_size\\\": \\\"\\\", \\\"min_component_size\\\": \\\"\\\"}\", \"uc_opt\": \"{\\\"no_correct\\\": \\\"false\\\", \\\"min_fasta_length\\\": \\\"\\\", \\\"mode\\\": \\\"normal\\\", \\\"no_pilon\\\": \\\"false\\\", \\\"no_rotate\\\": \\\"false\\\", \\\"lin_seq\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"\\\", \\\"contamination_fasta\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"paired_unpaired\": \"{\\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__job_resource\": \"{\\\"__current_case__\\\": 0, \\\"__job_resource__select\\\": \\\"no\\\"}\", \"rotation\": \"{\\\"start_gene_id\\\": \\\"\\\", \\\"start_gene_cov\\\": \\\"\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"chromInfo\": \"\\\"/galaxy-repl/localdata/chrom/?.len\\\"\", \"long_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"\\\"}\"}",
      "id": 5,
      "tool_shed_repository": {
        "owner": "iuc",
        "changeset_revision": "e9c1cdb9f9dc",
        "name": "unicycler",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "f469e49a-5729-4dbd-8f08-f5be3fca6191",
      "errors": null,
      "name": "Create assemblies with Unicycler",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "lr_align",
          "description": "runtime parameter for tool Create assemblies with Unicycler"
        },
        {
          "name": "paired_unpaired",
          "description": "runtime parameter for tool Create assemblies with Unicycler"
        },
        {
          "name": "paired_unpaired",
          "description": "runtime parameter for tool Create assemblies with Unicycler"
        },
        {
          "name": "rotation",
          "description": "runtime parameter for tool Create assemblies with Unicycler"
        },
        {
          "name": "long_reads",
          "description": "runtime parameter for tool Create assemblies with Unicycler"
        }
      ],
      "position": {
        "top": 609.9833374023438,
        "left": 725
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0",
      "type": "tool"
    },
    "6": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1.1",
      "tool_version": "4.1.1",
      "outputs": [
        {
          "type": "txt",
          "name": "quast_out"
        },
        {
          "type": "tsv",
          "name": "quast_tsv"
        },
        {
          "type": "tex",
          "name": "quast_tex"
        },
        {
          "type": "html",
          "name": "icarus"
        },
        {
          "type": "html",
          "name": "report_html"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "files_0|input": {
          "output_name": "assembly",
          "id": 5
        }
      },
      "tool_state": "{\"files\": \"[{\\\"type_file\\\": \\\"scaffold\\\", \\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"input_operon\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"threshold_contig\": \"\\\"0,1000\\\"\", \"__rerun_remap_job_id__\": null, \"annot\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_size\": \"\\\"\\\"\", \"input_ref\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy-repl/localdata/chrom/?.len\\\"\", \"min_contig\": \"\\\"500\\\"\", \"gene_selection\": \"\\\"prokaryotes\\\"\"}",
      "id": 6,
      "tool_shed_repository": {
        "owner": "iuc",
        "changeset_revision": "2f581f956e1c",
        "name": "quast",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "f20468eb-8292-4273-ac9e-b0d9c09b9e2e",
      "errors": "Tool is not installed.",
      "name": "Quast",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "input_operon",
          "description": "runtime parameter for tool Quast"
        },
        {
          "name": "annot",
          "description": "runtime parameter for tool Quast"
        },
        {
          "name": "input_ref",
          "description": "runtime parameter for tool Quast"
        }
      ],
      "position": {
        "top": 200,
        "left": 1145.9833984375
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1.1",
      "type": "tool"
    },
    "7": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0",
      "tool_version": "1.12.0",
      "outputs": [
        {
          "type": "gff",
          "name": "out_gff"
        },
        {
          "type": "txt",
          "name": "out_gbk"
        },
        {
          "type": "fasta",
          "name": "out_fna"
        },
        {
          "type": "fasta",
          "name": "out_faa"
        },
        {
          "type": "fasta",
          "name": "out_ffn"
        },
        {
          "type": "asn1",
          "name": "out_sqn"
        },
        {
          "type": "fasta",
          "name": "out_fsa"
        },
        {
          "type": "txt",
          "name": "out_tbl"
        },
        {
          "type": "txt",
          "name": "out_err"
        },
        {
          "type": "txt",
          "name": "out_txt"
        },
        {
          "type": "txt",
          "name": "out_log"
        }
      ],
      "workflow_outputs": [
        {
          "output_name": "out_ffn",
          "label": "ffn"
        },
        {
          "output_name": "out_gbk",
          "label": "gbk"
        },
        {
          "output_name": "out_tbl",
          "label": "tbl"
        }
      ],
      "input_connections": {
        "input": {
          "output_name": "assembly",
          "id": 5
        }
      },
      "tool_state": "{\"strain\": \"\\\"C\\\"\", \"increment\": \"\\\"10\\\"\", \"species\": \"\\\"Coli\\\"\", \"__page__\": null, \"usegenus\": \"\\\"true\\\"\", \"evalue\": \"\\\"1e-06\\\"\", \"compliant\": \"{\\\"mincontig\\\": \\\"200\\\", \\\"__current_case__\\\": 0, \\\"compliant_select\\\": \\\"no\\\", \\\"addgenes\\\": \\\"false\\\"}\", \"fast\": \"\\\"false\\\"\", \"__job_resource\": \"{\\\"__current_case__\\\": 0, \\\"__job_resource__select\\\": \\\"no\\\"}\", \"locustag\": \"\\\"PROKKA\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"kingdom\": \"{\\\"gcode\\\": \\\"11\\\", \\\"kingdom_select\\\": \\\"Bacteria\\\", \\\"__current_case__\\\": 1}\", \"metagenome\": \"\\\"false\\\"\", \"centre\": \"\\\"\\\"\", \"outputs\": \"[\\\"gff\\\", \\\"gbk\\\", \\\"fna\\\", \\\"faa\\\", \\\"ffn\\\", \\\"sqn\\\", \\\"fsa\\\", \\\"tbl\\\", \\\"err\\\", \\\"txt\\\"]\", \"gffver\": \"\\\"3\\\"\", \"norrna\": \"\\\"false\\\"\", \"proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"notrna\": \"\\\"false\\\"\", \"plasmid\": \"\\\"\\\"\", \"rfam\": \"\\\"false\\\"\", \"genus\": \"\\\"Escherichia\\\"\", \"chromInfo\": \"\\\"/galaxy-repl/localdata/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
      "id": 7,
      "tool_shed_repository": {
        "owner": "crs4",
        "changeset_revision": "a17498c603ec",
        "name": "prokka",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "9a6e8f35-351c-42c4-bbe0-9a9da64ae1a8",
      "errors": null,
      "name": "Prokka",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "input",
          "description": "runtime parameter for tool Prokka"
        },
        {
          "name": "proteins",
          "description": "runtime parameter for tool Prokka"
        }
      ],
      "position": {
        "top": 555,
        "left": 1100.9833984375
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0",
      "type": "tool"
    }
  },
  "annotation": "Unicycler with one tool deliberately removed to test missing-tool linting.",
  "a_galaxy_workflow": "true"
}

real-hacked-unicycler-assembly-testtoolshed.ga

Origin:

real-hacked

Format:

native

Path:

native/real-hacked-unicycler-assembly-testtoolshed.ga

Workflow Label:

Unicycler training

Description:

Unicycler with a test toolshed tool reference to test toolshed linting.

Python Tests:

• tests/test_lint.py

Interoperable Tests:

• test_lint_native_testtoolshed_warns (lint_native)

• test_unicycler_assembly_testtoolshed_valid_native (validate_native)

• test_unicycler_assembly_testtoolshed_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"Forward reads<br/><i>data</i>"]
    input_1>"Reverse Reads<br/><i>data</i>"]
    input_2>"Long Reads<br/><i>data</i>"]
    step_0["tool:testtoolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71"]
    step_1["tool:devteam/fastqc/fastqc/0.71"]
    step_2["tool:iuc/unicycler/unicycler/0.2.0"]
    step_3["tool:iuc/quast/quast/4.1.1"]
    step_4["tool:crs4/prokka/prokka/1.12.0"]
    input_0 --> step_0
    input_1 --> step_1
    input_1 --> step_2
    input_0 --> step_2
    input_2 --> step_2
    step_2 --> step_3
    step_2 --> step_4
    

Workflow source

{
  "uuid": "2fa1768f-116d-4695-83c5-6a07eff7be33",
  "tags": [],
  "format-version": "0.1",
  "name": "Unicycler training",
  "steps": {
    "0": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"forward_reads\"}",
      "id": 0,
      "uuid": "1e8ef78c-1cb2-4376-9fc5-3f9d47acfe69",
      "errors": null,
      "name": "Input dataset",
      "label": "Forward reads",
      "inputs": [
        {
          "name": "forward_reads",
          "description": ""
        }
      ],
      "position": {
        "top": 346,
        "left": 160.98333740234375
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "1": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"reverse_reads\"}",
      "id": 1,
      "uuid": "251d7a96-2b0d-4b8c-bf34-d24b65b32b41",
      "errors": null,
      "name": "Input dataset",
      "label": "Reverse Reads",
      "inputs": [
        {
          "name": "reverse_reads",
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}

real-hacked-unicycler-assembly-extra-annotations.ga

Origin:

real-hacked

Format:

native

Path:

native/real-hacked-unicycler-assembly-extra-annotations.ga

Workflow Label:

Unicycler training

Description:

Unicycler with extra step annotations for cytoscape visualization testing.

Python Tests:

• tests/test_cytoscape.py

Interoperable Tests:

• test_real_hacked_unicycler_repo_link_populated (cytoscape_elements_to_list)

• test_unicycler_assembly_extra_annotations_valid_native (validate_native)

• test_unicycler_assembly_extra_annotations_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"Forward reads<br/><i>data</i>"]
    input_1>"Reverse Reads<br/><i>data</i>"]
    input_2>"Long Reads<br/><i>data</i>"]
    step_0["fastQC"]
    step_1["tool:devteam/fastqc/fastqc/0.71"]
    step_2["tool:iuc/unicycler/unicycler/0.2.0"]
    step_3["tool:iuc/quast/quast/4.1.1"]
    step_4["tool:crs4/prokka/prokka/1.12.0"]
    input_0 --> step_0
    input_1 --> step_1
    input_1 --> step_2
    input_0 --> step_2
    input_2 --> step_2
    step_2 --> step_3
    step_2 --> step_4
    

Workflow source

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      "uuid": "1e8ef78c-1cb2-4376-9fc5-3f9d47acfe69",
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      "name": "Input dataset",
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      "inputs": [
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          "name": "forward_reads",
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      "annotation": "The forward reads (fastqsanger)",
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      "id": 1,
      "uuid": "251d7a96-2b0d-4b8c-bf34-d24b65b32b41",
      "errors": null,
      "name": "Input dataset",
      "label": "Reverse Reads",
      "inputs": [
        {
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          "description": ""
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      ],
      "position": {
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      "annotation": "The reverse reads (fastqsanger)",
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      "id": 2,
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      "errors": null,
      "name": "Input dataset",
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      "annotation": "The long reads (fastqsanger)",
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      "id": 3,
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      "errors": null,
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      "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0",
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          "type": "txt",
          "name": "assembly_grapth"
        },
        {
          "type": "fasta",
          "name": "assembly"
        }
      ],
      "workflow_outputs": [],
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        "long_reads": {
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real-sars-cov2-variant-calling.ga

Origin:

real

Format:

native

Path:

native/real-sars-cov2-variant-calling.ga

Workflow Label:

Download and SE+PE Illumina Covid Variation Workflow

Description:

Downloads reads from SRA and runs SE and PE COVID-19 variation workflows

Python Tests:

• tests/test_to_format2.py

• tests/test_to_native.py

• tests/test_export_abstract.py

Interoperable Tests:

• test_real_sars_cov2_smoke (cytoscape_node_ids)

• test_real_sars_cov2_shape (workflow_to_mermaid_lines)

• test_sars_cov2_variant_calling_rejected_native (validate_native)

• test_sars_cov2_variant_calling_rejected_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"Accessions file<br/><i>data</i>"]
    input_1>"NC_45512.2 fasta file<br/><i>data</i>"]
    step_0["0"]
    step_1["1"]
    step_2["2"]
    step_3["Merge filtered BAM files"]
    step_4["Merge fastp reports"]
    step_5["Merge samtools stats"]
    step_6["6"]
    step_7["tool:iuc/multiqc/multiqc/1.8+galaxy0"]
    step_8["SnpSift summary table"]
    input_0 --> step_0
    input_1 --> step_1
    step_0 --> step_1
    input_1 --> step_2
    step_0 --> step_2
    step_2 --> step_3
    step_1 --> step_3
    step_2 --> step_4
    step_1 --> step_4
    step_2 --> step_5
    step_1 --> step_5
    step_3 --> step_6
    input_1 --> step_6
    step_4 --> step_7
    step_5 --> step_7
    step_6 --> step_7
    step_6 --> step_8
    

Workflow source

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real-ecoli-comparison.ga

Origin:

real

Format:

native

Path:

native/real-ecoli-comparison.ga

Workflow Label:

ecoli-comparison

Description:

E. coli genome comparison workflow (has no declared outputs).

Python Tests:

• tests/test_lint.py

Interoperable Tests:

• test_ecoli_comparison_valid_native (validate_native)

• test_ecoli_comparison_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"_unlabeled_input_0<br/><i>data</i>"]
    input_1>"_unlabeled_input_1<br/><i>data</i>"]
    input_2>"_unlabeled_input_2<br/><i>collection</i>"]
    input_3>"_unlabeled_input_3<br/><i>collection</i>"]
    input_4>"_unlabeled_input_4<br/><i>collection</i>"]
    step_0["tool:nml/collapse_collections/collapse_dataset/4.0"]
    step_1["tool:bgruening/text_processing/tp_sed_tool/1.1.1"]
    step_2["tool:devteam/add_value/addValue/1.0.0"]
    step_3["tool:devteam/lastz/lastz_wrapper_2/1.3.2"]
    step_4["tool:random_lines1"]
    step_5["tool:Filter1"]
    step_6["tool:bgruening/text_processing/tp_grep_tool/1.1.1"]
    step_7["tool:bgruening/text_processing/tp_cat/0.1.0"]
    step_8["tool:Cut1"]
    step_9["tool:bgruening/text_processing/tp_sed_tool/1.1.1"]
    step_10["tool:iuc/datamash_ops/datamash_ops/1.1.0"]
    step_11["tool:devteam/fasta_compute_length/fasta_compute_length/1.0.1"]
    step_12["tool:nml/collapse_collections/collapse_dataset/4.0"]
    step_13["tool:devteam/merge_cols/mergeCols1/1.0.1"]
    step_14["tool:Grep1"]
    step_15["tool:bgruening/text_processing/tp_sort_header_tool/1.1.1"]
    step_16["tool:nml/collapse_collections/collapse_dataset/4.0"]
    step_17["tool:Cut1"]
    step_18["tool:Cut1"]
    step_19["tool:cat1"]
    step_20["tool:iuc/bedtools/bedtools_sortbed/2.27.0.0"]
    step_21["tool:iuc/bedtools/bedtools_complementbed/2.27.0.0"]
    step_22["tool:Filter1"]
    step_23["tool:Filter1"]
    step_24["tool:iuc/bedtools/bedtools_intersectbed/2.27.0.2"]
    step_25["tool:join1"]
    step_26["tool:devteam/fasta_filter_by_length/fasta_filter_by_length/1.1"]
    step_27["tool:devteam/lastz/lastz_wrapper_2/1.3.2"]
    step_28["tool:nml/collapse_collections/collapse_dataset/4.0"]
    step_29["tool:Grep1"]
    step_30["tool:bgruening/text_processing/tp_sed_tool/1.1.1"]
    step_27 --> step_0
    step_28 --> step_1
    step_29 --> step_2
    step_30 --> step_3
    input_3 --> step_3
    step_0 --> step_4
    step_0 --> step_5
    step_1 --> step_6
    step_1 --> step_7
    step_30 --> step_7
    step_2 --> step_8
    step_3 --> step_9
    step_5 --> step_10
    step_7 --> step_11
    step_8 --> step_12
    step_9 --> step_13
    step_10 --> step_14
    step_11 --> step_15
    step_13 --> step_16
    step_16 --> step_17
    step_16 --> step_18
    step_17 --> step_19
    step_18 --> step_19
    step_19 --> step_20
    step_15 --> step_21
    step_20 --> step_21
    step_21 --> step_22
    step_22 --> step_23
    step_23 --> step_24
    step_12 --> step_24
    step_24 --> step_25
    input_1 --> step_25
    input_0 --> step_26
    input_2 --> step_27
    input_0 --> step_27
    input_3 --> step_28
    input_4 --> step_29
    step_26 --> step_30
    

Workflow source

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  "annotation": "E. coli genome comparison workflow (has no declared outputs).",
  "format-version": "0.1",
  "name": "ecoli-comparison",
  "steps": {
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      "annotation": "",
      "content_id": null,
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      "tool_state": "{\"scoring\": \"{\\\"ambigIUPAC\\\": \\\"true\\\", \\\"ambigN\\\": \\\"false\\\", \\\"gap\\\": {\\\"__current_case__\\\": 1, \\\"gap_selector\\\": \\\"no\\\"}, \\\"match\\\": {\\\"__current_case__\\\": 1, \\\"match_selector\\\": \\\"no\\\"}, \\\"score_file\\\": null}\", \"__page__\": null, \"chaining\": \"{\\\"chain\\\": \\\"false\\\", \\\"chaning_penalties\\\": {\\\"__current_case__\\\": 0, \\\"anti\\\": \\\"\\\", \\\"chaning_penalties_selector\\\": \\\"yes\\\", \\\"diag\\\": \\\"\\\"}}\", \"output_format\": \"{\\\"out\\\": {\\\"__current_case__\\\": 4, \\\"format\\\": \\\"blastn\\\"}, \\\"rplot\\\": \\\"false\\\"}\", \"source\": \"{\\\"__current_case__\\\": 1, \\\"ref_source\\\": \\\"history\\\", \\\"target\\\": null}\", \"hsp\": \"{\\\"entropy\\\": \\\"false\\\", \\\"entropy_report\\\": \\\"false\\\", \\\"gfextend\\\": \\\"false\\\", \\\"hsp_method\\\": {\\\"__current_case__\\\": 0, \\\"hsp_method_selector\\\": \\\"none\\\"}, \\\"noentropy\\\": \\\"false\\\", \\\"nogfextend\\\": \\\"false\\\"}\", \"__rerun_remap_job_id__\": null, \"filters\": \"{\\\"continuity\\\": {\\\"cont_max\\\": \\\"\\\", \\\"cont_min\\\": \\\"\\\"}, \\\"coverage\\\": {\\\"cov_max\\\": \\\"\\\", \\\"cov_min\\\": \\\"\\\"}, \\\"filter_cgap\\\": \\\"\\\", \\\"filter_ngap\\\": \\\"\\\", \\\"filter_nmatch\\\": \\\"\\\", \\\"filter_nmatch_percent\\\": \\\"\\\", \\\"filter_nmismatch\\\": \\\"\\\", \\\"identity\\\": {\\\"id_max\\\": \\\"\\\", \\\"id_min\\\": \\\"\\\"}, \\\"notrivial\\\": \\\"false\\\"}\", \"query\": \"null\", \"where_to_look\": \"{\\\"nomirror\\\": \\\"false\\\", \\\"qdepth\\\": {\\\"__current_case__\\\": 1, \\\"qdepth_selector\\\": \\\"no\\\"}, \\\"qhspbest\\\": \\\"\\\", \\\"qhsplimit\\\": {\\\"__current_case__\\\": 1, \\\"qhsplimit_selector\\\": \\\"no\\\"}, \\\"self\\\": \\\"false\\\", \\\"strand\\\": \\\"--strand=both\\\"}\", \"interpolation\": \"{\\\"inner\\\": \\\"\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"query|__identifier__\": \"\\\"GCA_900157875.1\\\"\", \"seeding\": \"{\\\"seed\\\": {\\\"__current_case__\\\": 0, \\\"seed_selector\\\": \\\"defaults\\\"}, \\\"seed_filer\\\": {\\\"__current_case__\\\": 1, \\\"seed_filer_selector\\\": \\\"no\\\"}, \\\"transitions\\\": \\\"--transition\\\"}\", \"gap_ext\": \"{\\\"allgappedbounds\\\": \\\"false\\\", \\\"gapped\\\": \\\"false\\\", \\\"gappedthresh\\\": \\\"\\\", \\\"nogapped\\\": \\\"false\\\", \\\"noytrim\\\": \\\"false\\\", \\\"ydrop\\\": \\\"\\\"}\"}",
      "tool_version": "1.3.2",
      "type": "tool",
      "uuid": "5495b942-bbe1-4899-b131-5bb637ad00e5",
      "workflow_outputs": []
    },
    "7": {
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
      "errors": null,
      "id": 7,
      "input_connections": {
        "input_list": {
          "id": 3,
          "output_name": "output"
        }
      },
      "inputs": [],
      "label": null,
      "name": "Collapse Collection",
      "outputs": [
        {
          "name": "output",
          "type": "input"
        }
      ],
      "position": {
        "left": 230,
        "top": 250
      },
      "post_job_actions": {},
      "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
      "tool_shed_repository": {
        "changeset_revision": "25136a2b0cfe",
        "name": "collapse_collections",
        "owner": "nml",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "tool_state": "{\"__page__\": null, \"one_header\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"filename\": \"{\\\"__current_case__\\\": 1, \\\"add_name\\\": \\\"false\\\"}\", \"input_list\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
      "tool_version": "4.0",
      "type": "tool",
      "uuid": "faae8296-f402-4165-a758-03ca42b97b3e",
      "workflow_outputs": []
    },
    "8": {
      "annotation": "",
      "content_id": "Grep1",
      "errors": null,
      "id": 8,
      "input_connections": {
        "input": {
          "id": 4,
          "output_name": "output"
        }
      },
      "inputs": [],
      "label": null,
      "name": "Select",
      "outputs": [
        {
          "name": "out_file1",
          "type": "input"
        }
      ],
      "position": {
        "left": 230,
        "top": 370
      },
      "post_job_actions": {},
      "tool_id": "Grep1",
      "tool_state": "{\"__page__\": null, \"pattern\": \"\\\"^CDS\\\"\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input|__identifier__\": \"\\\"LT906474.1\\\"\"}",
      "tool_version": "1.0.1",
      "type": "tool",
      "uuid": "4c9bf0bb-88fe-45fc-9c5a-526ffa8ba881",
      "workflow_outputs": []
    },
    "9": {
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
      "errors": null,
      "id": 9,
      "input_connections": {
        "infile": {
          "id": 5,
          "output_name": "output"
        }
      },
      "inputs": [],
      "label": null,
      "name": "Text transformation",
      "outputs": [
        {
          "name": "output",
          "type": "input"
        }
      ],
      "position": {
        "left": 450,
        "top": 10
      },
      "post_job_actions": {},
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
      "tool_shed_repository": {
        "changeset_revision": "a6f147a050a2",
        "name": "text_processing",
        "owner": "bgruening",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "tool_state": "{\"__page__\": null, \"code\": \"\\\"s/^>1.*$/>Ecoli_C/\\\"\", \"adv_opts\": \"{\\\"__current_case__\\\": 0, \\\"adv_opts_selector\\\": \\\"basic\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}",
      "tool_version": "1.1.1",
      "type": "tool",
      "uuid": "240c3084-1de6-4149-abc8-a82c5fb1310c",
      "workflow_outputs": []
    }
  },
  "tags": [],
  "uuid": "7a9cf6a6-7dd6-48be-97c5-e443b785367c",
  "version": 0
}

real-shed-tools-raw.ga

Origin:

real

Format:

native

Path:

native/real-shed-tools-raw.ga

Workflow Label:

Workflow constructed from history ‘Cell paper’

Description:

Workflow with shed tool references and no declared outputs.

Python Tests:

• tests/test_lint.py

Interoperable Tests:

• test_lint_native_no_outputs_warns (lint_native)

• test_shed_tools_raw_valid_native (validate_native)

• test_shed_tools_raw_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37268/suppl/GSE37268%5Fmof3%2Eout%2Ehpeak%2Etxt%2E<br/><i>data</i>"]
    input_1>"Genes<br/><i>data</i>"]
    step_0["tool:bgruening/text_processing/tp_replace_in_column/1.1.0"]
    step_1["tool:devteam/get_flanks/get_flanks1/1.0.0"]
    step_2["tool:bgruening/text_processing/tp_replace_in_column/1.1.0"]
    step_3["tool:bgruening/text_processing/tp_replace_in_column/1.1.0"]
    step_4["tool:iuc/bedtools/bedtools_intersectbed/2.27.0.1"]
    step_5["tool:Grouping1"]
    input_0 --> step_0
    input_1 --> step_1
    step_0 --> step_2
    step_2 --> step_3
    step_1 --> step_4
    step_3 --> step_4
    step_4 --> step_5
    

Workflow source

{
  "uuid": "eb7fc9c5-992b-495a-9baa-4a9bb67d6262",
  "tags": [],
  "format-version": "0.1",
  "name": "Workflow constructed from history 'Cell paper'",
  "steps": {
    "0": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37268/suppl/GSE37268%5Fmof3%2Eout%2Ehpeak%2Etxt%2E\"}",
      "id": 0,
      "uuid": "4216f74b-f994-432a-b5be-2a6b981ac16a",
      "errors": null,
      "name": "Input dataset",
      "label": "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37268/suppl/GSE37268%5Fmof3%2Eout%2Ehpeak%2Etxt%2E",
      "inputs": [
        {
          "name": "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37268/suppl/GSE37268%5Fmof3%2Eout%2Ehpeak%2Etxt%2E",
          "description": ""
        }
      ],
      "position": {
        "top": 335,
        "left": 200
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "1": {
      "tool_id": null,
      "tool_version": null,
      "outputs": [],
      "workflow_outputs": [],
      "input_connections": {},
      "tool_state": "{\"name\": \"Genes\"}",
      "id": 1,
      "uuid": "0d2e344b-fd58-462c-bd21-c60acd045d9d",
      "errors": null,
      "name": "Input dataset",
      "label": "Genes",
      "inputs": [
        {
          "name": "Genes",
          "description": ""
        }
      ],
      "position": {
        "top": 455,
        "left": 200
      },
      "annotation": "",
      "content_id": null,
      "type": "data_input"
    },
    "2": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0",
      "tool_version": "1.1.0",
      "outputs": [
        {
          "type": "input",
          "name": "outfile"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "infile": {
          "output_name": "output",
          "id": 0
        }
      },
      "tool_state": "{\"__page__\": null, \"find_pattern\": \"\\\"[0-9]+\\\"\", \"column\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"replace_pattern\": \"\\\"chr&\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 2,
      "tool_shed_repository": {
        "owner": "bgruening",
        "changeset_revision": "20344ce0c811",
        "name": "text_processing",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "d40b3d69-2a99-4b00-bf75-7ded995dfbd7",
      "errors": null,
      "name": "Replace Text",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "infile",
          "description": "runtime parameter for tool Replace Text"
        }
      ],
      "position": {
        "top": 335,
        "left": 420
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0",
      "type": "tool"
    },
    "3": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0",
      "tool_version": "1.0.0",
      "outputs": [
        {
          "type": "input",
          "name": "out_file1"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "input": {
          "output_name": "output",
          "id": 1
        }
      },
      "tool_state": "{\"__page__\": null, \"direction\": \"\\\"Upstream\\\"\", \"region\": \"\\\"start\\\"\", \"offset\": \"\\\"10000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"__rerun_remap_job_id__\": null, \"size\": \"\\\"12000\\\"\"}",
      "id": 3,
      "tool_shed_repository": {
        "owner": "devteam",
        "changeset_revision": "077f404ae1bb",
        "name": "get_flanks",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "652af7e8-710b-4476-952f-484d6a2e4a7a",
      "errors": null,
      "name": "Get flanks",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "input",
          "description": "runtime parameter for tool Get flanks"
        }
      ],
      "position": {
        "top": 475,
        "left": 415
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0",
      "type": "tool"
    },
    "4": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0",
      "tool_version": "1.1.0",
      "outputs": [
        {
          "type": "input",
          "name": "outfile"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "infile": {
          "output_name": "outfile",
          "id": 2
        }
      },
      "tool_state": "{\"__page__\": null, \"find_pattern\": \"\\\"chr20\\\"\", \"column\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"replace_pattern\": \"\\\"chrX\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 4,
      "tool_shed_repository": {
        "owner": "bgruening",
        "changeset_revision": "20344ce0c811",
        "name": "text_processing",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "37f15259-3b03-4461-8da3-6e8ee34fd2f5",
      "errors": null,
      "name": "Replace Text",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "infile",
          "description": "runtime parameter for tool Replace Text"
        }
      ],
      "position": {
        "top": 335,
        "left": 640
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0",
      "type": "tool"
    },
    "5": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0",
      "tool_version": "1.1.0",
      "outputs": [
        {
          "type": "input",
          "name": "outfile"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "infile": {
          "output_name": "outfile",
          "id": 4
        }
      },
      "tool_state": "{\"__page__\": null, \"find_pattern\": \"\\\"chr21\\\"\", \"column\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"replace_pattern\": \"\\\"chrY\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
      "id": 5,
      "tool_shed_repository": {
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        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "8ce00200-94b7-4daf-a0e5-e3b8d6d87eeb",
      "errors": null,
      "name": "Replace Text",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "infile",
          "description": "runtime parameter for tool Replace Text"
        }
      ],
      "position": {
        "top": 335,
        "left": 860
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0",
      "type": "tool"
    },
    "6": {
      "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1",
      "tool_version": "2.27.0.1",
      "outputs": [
        {
          "type": "input",
          "name": "output"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "inputA": {
          "output_name": "out_file1",
          "id": 3
        },
        "reduce_or_iterate|inputB": {
          "output_name": "outfile",
          "id": 5
        }
      },
      "tool_state": "{\"count\": \"\\\"false\\\"\", \"__page__\": null, \"reciprocal\": \"\\\"false\\\"\", \"overlap_mode\": \"\\\"-wa\\\"\", \"invert\": \"\\\"false\\\"\", \"header\": \"\\\"false\\\"\", \"inputA\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 6112359}]}\", \"reduce_or_iterate\": \"{\\\"inputB\\\": {\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 6112359}]}, \\\"reduce_or_iterate_selector\\\": \\\"iterate\\\", \\\"__current_case__\\\": 0}\", \"split\": \"\\\"false\\\"\", \"fraction\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"strand\": \"\\\"\\\"\", \"once\": \"\\\"false\\\"\"}",
      "id": 6,
      "tool_shed_repository": {
        "owner": "iuc",
        "changeset_revision": "33c3ddea63c5",
        "name": "bedtools",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "uuid": "c65fd1f5-9fc2-4acf-96c6-94ea61906042",
      "errors": null,
      "name": "Intersect intervals",
      "post_job_actions": {},
      "label": null,
      "inputs": [],
      "position": {
        "top": 655,
        "left": 1022
      },
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1",
      "type": "tool"
    },
    "7": {
      "tool_id": "Grouping1",
      "tool_version": "2.1.1",
      "outputs": [
        {
          "type": "tabular",
          "name": "out_file1"
        }
      ],
      "workflow_outputs": [],
      "input_connections": {
        "input1": {
          "output_name": "output",
          "id": 6
        }
      },
      "tool_state": "{\"operations\": \"[{\\\"opcol\\\": \\\"1\\\", \\\"__index__\\\": 0, \\\"optype\\\": \\\"length\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"ignorelines\": \"null\", \"groupcol\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"false\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}",
      "id": 7,
      "uuid": "be264526-e498-4050-b6cd-f7a842268d4a",
      "errors": null,
      "name": "Group",
      "post_job_actions": {},
      "label": null,
      "inputs": [
        {
          "name": "input1",
          "description": "runtime parameter for tool Group"
        }
      ],
      "position": {
        "top": 335,
        "left": 1300
      },
      "annotation": "",
      "content_id": "Grouping1",
      "type": "tool"
    }
  },
  "annotation": "Workflow with shed tool references and no declared outputs.",
  "a_galaxy_workflow": "true"
}

real-multi-data-input.ga

Origin:

real

Format:

native

Path:

native/real-multi-data-input.ga

Workflow Label:

Multi-data input

Description:

Workflow demonstrating multi-file dataset input.

Python Tests:

• tests/test_to_format2.py

Mermaid diagram

        graph LR
    input_0>"optional<br/><i>data</i>"]
    input_1>"required<br/><i>data</i>"]
    step_0["count_multi_file"]
    input_1 --> step_0
    input_0 --> step_0
    

Workflow source

{
  "steps": {
    "0": {
      "optional": true,
      "type": "data_input",
      "label": "optional",
      "id": 0,
      "position": {
        "left": 0,
        "top": 0
      },
      "annotation": "",
      "input_connections": {},
      "inputs": [
        {
          "name": "optional",
          "description": ""
        }
      ],
      "tool_state": "{\"name\": \"optional\", \"optional\": true}"
    },
    "1": {
      "optional": false,
      "type": "data_input",
      "label": "required",
      "id": 1,
      "position": {
        "left": 10,
        "top": 10
      },
      "annotation": "",
      "input_connections": {},
      "inputs": [
        {
          "name": "required",
          "description": ""
        }
      ],
      "tool_state": "{\"name\": \"required\", \"optional\": false}"
    },
    "2": {
      "tool_id": "count_multi_file",
      "label": "count_multi_file",
      "id": 2,
      "position": {
        "left": 20,
        "top": 20
      },
      "type": "tool",
      "name": "count_multi_file",
      "post_job_actions": {},
      "tool_version": null,
      "annotation": "",
      "input_connections": {
        "input1": [
          {
            "id": 1,
            "output_name": "output"
          },
          {
            "id": 0,
            "output_name": "output"
          }
        ]
      },
      "tool_state": "{\"__page__\": 0}"
    }
  },
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Multi-data input",
  "uuid": "23584e0c-59c3-4849-b703-853ef8883c99",
  "annotation": "Workflow demonstrating multi-file dataset input."
}

real-multi-string-input.ga

Origin:

real

Format:

native

Path:

native/real-multi-string-input.ga

Workflow Label:

multi-text

Description:

Workflow demonstrating multi-string parameter input.

Python Tests:

• tests/test_to_format2.py

Interoperable Tests:

• test_multi_string_input_valid_native (validate_native)

• test_multi_string_input_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"multi-text<br/><i>string</i>"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "multi-text",
  "steps": {
    "0": {
      "annotation": "",
      "content_id": null,
      "errors": null,
      "id": 0,
      "input_connections": {},
      "inputs": [
        {
          "description": "",
          "name": "multi-text"
        }
      ],
      "label": "multi-text",
      "name": "Input parameter",
      "outputs": [],
      "position": {
        "left": 0,
        "top": 0
      },
      "tool_id": null,
      "tool_state": "{\"multiple\": true, \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
      "tool_version": null,
      "type": "parameter_input",
      "uuid": "5410bc57-d24c-4818-9a0c-9f9ba6857584",
      "when": null,
      "workflow_outputs": []
    }
  },
  "annotation": "Workflow demonstrating multi-string parameter input."
}

real-basic-without-step-input-label.ga

Origin:

real

Format:

native

Path:

native/real-basic-without-step-input-label.ga

Workflow Label:

Simple workflow

Description:

Simple workflow that no-op cats a file and then selects 10 random lines.

Python Tests:

• tests/test_to_format2.py

• tests/test_export_abstract.py

Interoperable Tests:

• test_basic_without_step_input_label_valid_native (validate_native)

• test_basic_without_step_input_label_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"_unlabeled_input_0<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

{
  "steps": {
    "0": {
      "type": "data_input",
      "label": null,
      "id": 0,
      "position": {
        "left": 0,
        "top": 0
      },
      "annotation": "input doc",
      "input_connections": {},
      "inputs": [
        {
          "name": "the_input",
          "description": ""
        }
      ],
      "tool_state": "{\"name\": \"the_input\"}"
    },
    "1": {
      "tool_id": "cat1",
      "label": "cat",
      "id": 1,
      "position": {
        "left": 10,
        "top": 10
      },
      "type": "tool",
      "name": "cat1",
      "post_job_actions": {},
      "tool_version": null,
      "annotation": "cat doc",
      "input_connections": {
        "input1": [
          {
            "id": 0,
            "output_name": "output"
          }
        ]
      },
      "tool_state": "{\"__page__\": 0}",
      "workflow_outputs": [
        {
          "output_name": "out_file1",
          "label": "the_output",
          "uuid": null
        }
      ]
    }
  },
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Simple workflow",
  "uuid": "f7f9fdbe-fb11-4721-be02-097709beb86f",
  "annotation": "Simple workflow that no-op cats a file and then selects 10 random lines.\n"
}

synthetic-unlinted-best-practices.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-unlinted-best-practices.ga

Workflow Label:

bp (imported from uploaded file)

Python Tests:

• tests/test_lint_best_practices.py

Interoperable Tests:

• test_bp_native_untyped_param (lint_best_practices_native)

• test_bp_native_disconnected_input (lint_best_practices_native)

• test_bp_native_untyped_pja (lint_best_practices_native)

• test_extra_position_fields_stripped (normalized_native)

• test_unlinted_best_practices_valid_native (validate_native)

• test_unlinted_best_practices_rejected_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"_unlabeled_input_0<br/><i>data</i>"]
    step_0["tool:bgruening/text_processing/tp_replace_in_column/1.1.3"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "annotation": "",
  "format-version": "0.1",
  "name": "bp (imported from uploaded file)",
  "steps": {
    "0": {
      "annotation": "",
      "content_id": null,
      "errors": null,
      "id": 0,
      "input_connections": {},
      "inputs": [],
      "label": null,
      "name": "Input dataset",
      "outputs": [],
      "position": {
        "bottom": 730.3166656494141,
        "height": 82.55000305175781,
        "left": 1155,
        "right": 1355,
        "top": 647.7666625976562,
        "width": 200,
        "x": 1155,
        "y": 647.7666625976562
      },
      "tool_id": null,
      "tool_state": "{\"optional\": false}",
      "tool_version": null,
      "type": "data_input",
      "uuid": "4219d43a-e182-49c0-bee3-8422e6344911",
      "workflow_outputs": []
    },
    "1": {
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
      "errors": null,
      "id": 1,
      "input_connections": {},
      "inputs": [
        {
          "description": "runtime parameter for tool Replace Text",
          "name": "infile"
        }
      ],
      "label": null,
      "name": "Replace Text",
      "outputs": [
        {
          "name": "outfile",
          "type": "input"
        }
      ],
      "position": {
        "bottom": 744.8333282470703,
        "height": 114.06666564941406,
        "left": 1465,
        "right": 1665,
        "top": 630.7666625976562,
        "width": 200,
        "x": 1465,
        "y": 630.7666625976562
      },
      "post_job_actions": {
        "TagDatasetActionoutfile": {
          "action_arguments": {
            "tags": "${report_name}"
          },
          "action_type": "TagDatasetAction",
          "output_name": "outfile"
        }
      },
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
      "tool_shed_repository": {
        "changeset_revision": "ddf54b12c295",
        "name": "text_processing",
        "owner": "bgruening",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"${report_name}\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
      "tool_version": "1.1.3",
      "type": "tool",
      "uuid": "e429e21f-f01e-4efb-b665-56f454cbe38b",
      "workflow_outputs": [
        {
          "label": null,
          "output_name": "outfile",
          "uuid": "e4066fe7-c9a2-43af-a9f5-30a75a5b2107"
        }
      ]
    }
  },
  "tags": [],
  "uuid": "66708ffe-c08c-4647-a7e9-fc7f731206a1",
  "version": 2
}

synthetic-unlinted-best-practices-dict-tool-state.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-unlinted-best-practices-dict-tool-state.ga

Workflow Label:

bp (imported from uploaded file)

Python Tests:

• tests/test_lint_best_practices.py

Interoperable Tests:

• test_unlinted_best_practices_dict_tool_state_valid_native (validate_native)

• test_unlinted_best_practices_dict_tool_state_rejected_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"_unlabeled_input_0<br/><i>data</i>"]
    step_0["tool:bgruening/text_processing/tp_replace_in_column/1.1.3"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "annotation": "",
  "format-version": "0.1",
  "name": "bp (imported from uploaded file)",
  "steps": {
    "0": {
      "annotation": "",
      "content_id": null,
      "errors": null,
      "id": 0,
      "input_connections": {},
      "inputs": [],
      "label": null,
      "name": "Input dataset",
      "outputs": [],
      "position": {
        "bottom": 730.3166656494141,
        "height": 82.55000305175781,
        "left": 1155,
        "right": 1355,
        "top": 647.7666625976562,
        "width": 200,
        "x": 1155,
        "y": 647.7666625976562
      },
      "tool_id": null,
      "tool_state": {
        "optional": false
      },
      "tool_version": null,
      "type": "data_input",
      "uuid": "4219d43a-e182-49c0-bee3-8422e6344911",
      "workflow_outputs": []
    },
    "1": {
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
      "errors": null,
      "id": 1,
      "input_connections": {},
      "inputs": [
        {
          "description": "runtime parameter for tool Replace Text",
          "name": "infile"
        }
      ],
      "label": null,
      "name": "Replace Text",
      "outputs": [
        {
          "name": "outfile",
          "type": "input"
        }
      ],
      "position": {
        "bottom": 744.8333282470703,
        "height": 114.06666564941406,
        "left": 1465,
        "right": 1665,
        "top": 630.7666625976562,
        "width": 200,
        "x": 1465,
        "y": 630.7666625976562
      },
      "post_job_actions": {
        "TagDatasetActionoutfile": {
          "action_arguments": {
            "tags": "${report_name}"
          },
          "action_type": "TagDatasetAction",
          "output_name": "outfile"
        }
      },
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
      "tool_shed_repository": {
        "changeset_revision": "ddf54b12c295",
        "name": "text_processing",
        "owner": "bgruening",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "tool_state": {
        "infile": {
          "__class__": "RuntimeValue"
        },
        "replacements": [
          {
            "__index__": 0,
            "column": "1",
            "find_pattern": "${report_name}",
            "replace_pattern": ""
          }
        ],
        "__page__": null,
        "__rerun_remap_job_id__": null
      },
      "tool_version": "1.1.3",
      "type": "tool",
      "uuid": "e429e21f-f01e-4efb-b665-56f454cbe38b",
      "workflow_outputs": [
        {
          "label": null,
          "output_name": "outfile",
          "uuid": "e4066fe7-c9a2-43af-a9f5-30a75a5b2107"
        }
      ]
    }
  },
  "tags": [],
  "uuid": "66708ffe-c08c-4647-a7e9-fc7f731206a1",
  "version": 2
}

synthetic-unlinted-best-practices-bad-identifier.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-unlinted-best-practices-bad-identifier.ga

Workflow Label:

bp (imported from uploaded file)

Python Tests:

• tests/test_lint_best_practices.py

Interoperable Tests:

• test_bp_native_bad_creator_id (lint_best_practices_native)

• test_unlinted_best_practices_bad_identifier_valid_native (validate_native)

• test_unlinted_best_practices_bad_identifier_rejected_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"_unlabeled_input_0<br/><i>data</i>"]
    step_0["tool:bgruening/text_processing/tp_replace_in_column/1.1.3"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "annotation": "",
  "format-version": "0.1",
  "name": "bp (imported from uploaded file)",
  "creator": [
    {
      "class": "Person",
      "identifier": "0000-0002-1825-0097",
      "name": "Josiah Carberry",
      "url": "https://orcid.org/0000-0002-1825-0097"
    }
  ],
  "steps": {
    "0": {
      "annotation": "",
      "content_id": null,
      "errors": null,
      "id": 0,
      "input_connections": {},
      "inputs": [],
      "label": null,
      "name": "Input dataset",
      "outputs": [],
      "position": {
        "bottom": 730.3166656494141,
        "height": 82.55000305175781,
        "left": 1155,
        "right": 1355,
        "top": 647.7666625976562,
        "width": 200,
        "x": 1155,
        "y": 647.7666625976562
      },
      "tool_id": null,
      "tool_state": "{\"optional\": false}",
      "tool_version": null,
      "type": "data_input",
      "uuid": "4219d43a-e182-49c0-bee3-8422e6344911",
      "workflow_outputs": []
    },
    "1": {
      "annotation": "",
      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
      "errors": null,
      "id": 1,
      "input_connections": {},
      "inputs": [
        {
          "description": "runtime parameter for tool Replace Text",
          "name": "infile"
        }
      ],
      "label": null,
      "name": "Replace Text",
      "outputs": [
        {
          "name": "outfile",
          "type": "input"
        }
      ],
      "position": {
        "bottom": 744.8333282470703,
        "height": 114.06666564941406,
        "left": 1465,
        "right": 1665,
        "top": 630.7666625976562,
        "width": 200,
        "x": 1465,
        "y": 630.7666625976562
      },
      "post_job_actions": {
        "TagDatasetActionoutfile": {
          "action_arguments": {
            "tags": "${report_name}"
          },
          "action_type": "TagDatasetAction",
          "output_name": "outfile"
        }
      },
      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
      "tool_shed_repository": {
        "changeset_revision": "ddf54b12c295",
        "name": "text_processing",
        "owner": "bgruening",
        "tool_shed": "toolshed.g2.bx.psu.edu"
      },
      "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"${report_name}\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
      "tool_version": "1.1.3",
      "type": "tool",
      "uuid": "e429e21f-f01e-4efb-b665-56f454cbe38b",
      "workflow_outputs": [
        {
          "label": null,
          "output_name": "outfile",
          "uuid": "e4066fe7-c9a2-43af-a9f5-30a75a5b2107"
        }
      ]
    }
  },
  "tags": [],
  "uuid": "8c13f49c-c0c2-4f3a-85d7-5bad6be1776f",
  "version": 2
}

synthetic-minimal-tool.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-minimal-tool.ga

Workflow Label:

Test

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_ensure_native_normalizes_native (ensure_native)

• test_bp_native_no_annotation (lint_best_practices_native)

• test_bp_native_no_creator (lint_best_practices_native)

• test_bp_native_no_license (lint_best_practices_native)

• test_bp_native_step_no_label (lint_best_practices_native)

• test_lint_native_minimal_no_outputs (lint_native)

• test_tool_state_always_dict (normalized_native)

• test_containers_never_none (normalized_native)

• test_tags_never_none (normalized_native)

• test_connected_paths_empty (normalized_native)

• test_single_tool_native (normalized_native)

• test_minimal_valid_native (validate_native)

• test_minimal_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    step_0["tool:cat1"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Test",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1",
      "tool_version": "1.0",
      "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}}"
    }
  }
}

synthetic-inner-subworkflow.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-inner-subworkflow.ga

Workflow Label:

Inner

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_inner_subworkflow_valid_native (validate_native)

• test_inner_subworkflow_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"inner_input<br/><i>data</i>"]
    step_0["tool:random_lines1"]
    input_0 --> step_0
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Inner",
  "steps": {
    "0": {
      "id": 0,
      "type": "data_input",
      "label": "inner_input",
      "tool_state": "{}",
      "input_connections": {},
      "inputs": [],
      "outputs": [],
      "workflow_outputs": []
    },
    "1": {
      "id": 1,
      "type": "tool",
      "tool_id": "random_lines1",
      "input_connections": {
        "input": {
          "id": 0,
          "output_name": "output"
        }
      }
    }
  }
}

synthetic-native-data-input.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-native-data-input.ga

Workflow Label:

Test

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_no_tool_steps_native (normalized_native)

• test_native_data_input_valid_native (validate_native)

• test_native_data_input_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"inp<br/><i>data</i>"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Test",
  "steps": {
    "0": {
      "id": 0,
      "type": "data_input",
      "label": "inp",
      "tool_state": "{}",
      "input_connections": {},
      "inputs": [],
      "outputs": [],
      "workflow_outputs": []
    }
  }
}

synthetic-outer-inline-subworkflow.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-outer-inline-subworkflow.ga

Workflow Label:

Outer

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_inline_subworkflow_expanded (expanded_native)

• test_to_format2_inline_subworkflow (to_format2)

• test_outer_inline_subworkflow_valid_native (validate_native)

• test_outer_inline_subworkflow_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"inp<br/><i>data</i>"]
    step_0["0"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Outer",
  "steps": {
    "0": {
      "id": 0,
      "type": "data_input",
      "label": "inp",
      "tool_state": "{}"
    },
    "1": {
      "id": 1,
      "type": "subworkflow",
      "subworkflow": {
        "a_galaxy_workflow": "true",
        "format-version": "0.1",
        "name": "Inner",
        "steps": {
          "0": {
            "id": 0,
            "type": "data_input",
            "label": "inner_input",
            "tool_state": "{}",
            "input_connections": {},
            "inputs": [],
            "outputs": [],
            "workflow_outputs": []
          },
          "1": {
            "id": 1,
            "type": "tool",
            "tool_id": "random_lines1",
            "input_connections": {
              "input": {
                "id": 0,
                "output_name": "output"
              }
            }
          }
        }
      }
    }
  }
}

synthetic-outer-url-subworkflow.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-outer-url-subworkflow.ga

Workflow Label:

Outer

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_to_format2_url_subworkflow (to_format2)

• test_outer_url_subworkflow_valid_native (validate_native)

• test_outer_url_subworkflow_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"inp<br/><i>data</i>"]
    step_0["0"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Outer",
  "steps": {
    "0": {
      "id": 0,
      "type": "data_input",
      "label": "inp",
      "tool_state": "{}"
    },
    "1": {
      "id": 1,
      "type": "subworkflow",
      "content_id": "https://example.com/inner.ga"
    }
  }
}

synthetic-native-tool-with-subworkflow.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-native-tool-with-subworkflow.ga

Workflow Label:

Outer

Python Tests:

• tests/test_normalized.py

Interoperable Tests:

• test_inline_subworkflow_native (normalized_native)

• test_native_tool_with_subworkflow_valid_native (validate_native)

• test_native_tool_with_subworkflow_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    step_0["tool:cat1"]
    step_1["1"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Outer",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1",
      "tool_version": "1.0",
      "tool_state": "{}",
      "input_connections": {},
      "inputs": [],
      "outputs": [],
      "workflow_outputs": []
    },
    "1": {
      "id": 1,
      "type": "subworkflow",
      "tool_state": "{}",
      "input_connections": {},
      "inputs": [],
      "outputs": [],
      "workflow_outputs": [],
      "subworkflow": {
        "a_galaxy_workflow": "true",
        "format-version": "0.1",
        "name": "Inner",
        "steps": {
          "0": {
            "id": 0,
            "type": "tool",
            "tool_id": "sort1",
            "tool_version": "2.0",
            "tool_state": "{}",
            "input_connections": {},
            "inputs": [],
            "outputs": [],
            "workflow_outputs": []
          }
        }
      }
    }
  }
}

synthetic-labeled-tool.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-labeled-tool.ga

Workflow Label:

Test Workflow

Description:

A test workflow

Interoperable Tests:

• test_ensure_format2_converts_native (ensure_format2)

• test_to_format2_metadata (to_format2)

• test_to_format2_inputs (to_format2)

• test_to_format2_outputs (to_format2)

• test_to_format2_tool_step (to_format2)

• test_to_format2_step_inputs (to_format2)

• test_labeled_tool_valid_native (validate_native)

• test_labeled_tool_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"the_input<br/><i>data</i>"]
    step_0["the_cat"]
    input_0 --> step_0
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Test Workflow",
  "annotation": "A test workflow",
  "steps": {
    "0": {
      "id": 0,
      "type": "data_input",
      "label": "the_input",
      "tool_state": "{\"optional\": false}",
      "input_connections": {},
      "inputs": [
        {
          "name": "the_input",
          "description": ""
        }
      ],
      "outputs": [],
      "workflow_outputs": []
    },
    "1": {
      "id": 1,
      "type": "tool",
      "tool_id": "cat1",
      "tool_version": "1.0",
      "label": "the_cat",
      "input_connections": {
        "input1": {
          "id": 0,
          "output_name": "output"
        }
      },
      "workflow_outputs": [
        {
          "output_name": "out_file1",
          "label": "the_output"
        }
      ]
    }
  }
}

synthetic-rename-pja.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-rename-pja.ga

Workflow Label:

PJA Test

Interoperable Tests:

• test_to_format2_rename_pja (to_format2)

• test_rename_pja_valid_native (validate_native)

• test_rename_pja_valid_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    input_0>"inp<br/><i>data</i>"]
    step_0["cat"]
    input_0 --> step_0
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "PJA Test",
  "steps": {
    "0": {
      "id": 0,
      "type": "data_input",
      "label": "inp",
      "tool_state": "{}",
      "input_connections": {},
      "inputs": [],
      "outputs": [],
      "workflow_outputs": []
    },
    "1": {
      "id": 1,
      "type": "tool",
      "tool_id": "cat1",
      "label": "cat",
      "input_connections": {
        "input1": {
          "id": 0,
          "output_name": "output"
        }
      },
      "post_job_actions": {
        "RenameDatasetActionout_file1": {
          "action_type": "RenameDatasetAction",
          "output_name": "out_file1",
          "action_arguments": {
            "newname": "renamed_output"
          }
        }
      }
    }
  }
}

synthetic-extra-field.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-extra-field.ga

Workflow Label:

Extra field native

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_extra_field_valid_native_lax (validate_native)

• test_extra_field_rejected_native_strict (validate_native_strict)

Mermaid diagram

        graph LR
    step_0["tool:cat1"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Extra field native",
  "not_a_real_field": "should cause strict validation failure",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1"
    }
  }
}

synthetic-missing-marker.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-missing-marker.ga

Workflow Label:

Missing a_galaxy_workflow marker

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_lint_native_missing_marker (lint_native)

• test_missing_marker_rejected_native (validate_native)

• test_missing_marker_rejected_native_strict (validate_native_strict)

Workflow source

{
  "format-version": "0.1",
  "name": "Missing a_galaxy_workflow marker",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1"
    }
  }
}

real-hacked-basic-missing-format-version.ga

Origin:

real-hacked

Format:

native

Path:

native/real-hacked-basic-missing-format-version.ga

Workflow Label:

Simple workflow

Description:

Simple workflow that no-op cats a file and then selects 10 random lines.

Python Tests:

• tests/test_schema_rules_catalog.py

Workflow source

{
  "steps": {
    "0": {
      "type": "data_input",
      "label": null,
      "id": 0,
      "position": {
        "left": 0,
        "top": 0
      },
      "annotation": "input doc",
      "input_connections": {},
      "inputs": [
        {
          "name": "the_input",
          "description": ""
        }
      ],
      "tool_state": "{\"name\": \"the_input\"}"
    },
    "1": {
      "tool_id": "cat1",
      "label": "cat",
      "id": 1,
      "position": {
        "left": 10,
        "top": 10
      },
      "type": "tool",
      "name": "cat1",
      "post_job_actions": {},
      "tool_version": null,
      "annotation": "cat doc",
      "input_connections": {
        "input1": [
          {
            "id": 0,
            "output_name": "output"
          }
        ]
      },
      "tool_state": "{\"__page__\": 0}",
      "workflow_outputs": [
        {
          "output_name": "out_file1",
          "label": "the_output",
          "uuid": null
        }
      ]
    }
  },
  "a_galaxy_workflow": "true",
  "name": "Simple workflow",
  "uuid": "f7f9fdbe-fb11-4721-be02-097709beb86f",
  "annotation": "Simple workflow that no-op cats a file and then selects 10 random lines.\n"
}

synthetic-lint-no-steps.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-no-steps.ga

Workflow Label:

Missing steps

Interoperable Tests:

• test_lint_native_missing_steps (lint_native)

Mermaid diagram

        graph LR
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Missing steps"
}

synthetic-lint-bad-format-version.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-bad-format-version.ga

Workflow Label:

Bad format version

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_lint_native_bad_format_version (lint_native)

• test_bad_format_version_rejected_native (validate_native)

• test_bad_format_version_rejected_native_strict (validate_native_strict)

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.2",
  "name": "Bad format version",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1"
    }
  }
}

synthetic-lint-bad-marker.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-bad-marker.ga

Workflow Label:

Bad marker value

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_lint_native_bad_marker (lint_native)

• test_bad_marker_rejected_native (validate_native)

• test_bad_marker_rejected_native_strict (validate_native_strict)

Workflow source

{
  "a_galaxy_workflow": "false",
  "format-version": "0.1",
  "name": "Bad marker value",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1"
    }
  }
}

synthetic-lint-non-integer-step.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-non-integer-step.ga

Workflow Label:

Non-integer step key

Interoperable Tests:

• test_lint_native_non_integer_step_key (lint_native)

Mermaid diagram

        graph LR
    step_0["0"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Non-integer step key",
  "steps": {
    "step_one": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1"
    }
  }
}

synthetic-lint-nested-no-steps.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-nested-no-steps.ga

Workflow Label:

Nested subworkflow missing steps

Interoperable Tests:

• test_lint_native_nested_no_steps (lint_native)

Mermaid diagram

        graph LR
    step_0["0"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Nested subworkflow missing steps",
  "steps": {
    "0": {
      "id": 0,
      "type": "subworkflow",
      "subworkflow": {
        "a_galaxy_workflow": "true",
        "format-version": "0.1",
        "name": "Inner",
        "steps": {}
      }
    }
  }
}

synthetic-lint-output-no-label.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-output-no-label.ga

Workflow Label:

Output without label

Interoperable Tests:

• test_lint_native_output_no_label (lint_native)

Mermaid diagram

        graph LR
    step_0["tool:cat1"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Output without label",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1",
      "workflow_outputs": [
        {
          "output_name": "out_file1"
        }
      ]
    }
  }
}

synthetic-lint-report.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-report.ga

Workflow Label:

Workflow with report

Interoperable Tests:

• test_lint_native_report_clean (lint_native)

Mermaid diagram

        graph LR
    step_0["tool:cat1"]
    

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Workflow with report",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1",
      "workflow_outputs": [
        {
          "label": "the_output",
          "output_name": "out_file1"
        }
      ]
    }
  },
  "report": {
    "markdown": "# Workflow Report\nSome text.\n"
  }
}

synthetic-lint-report-bad-type.ga

Origin:

synthetic

Format:

native

Path:

native/synthetic-lint-report-bad-type.ga

Workflow Label:

Report with bad markdown type

Python Tests:

• tests/test_schema_rules_catalog.py

Interoperable Tests:

• test_report_bad_type_rejected_native (validate_native)

• test_report_bad_type_rejected_native_strict (validate_native_strict)

Workflow source

{
  "a_galaxy_workflow": "true",
  "format-version": "0.1",
  "name": "Report with bad markdown type",
  "steps": {
    "0": {
      "id": 0,
      "type": "tool",
      "tool_id": "cat1",
      "workflow_outputs": [
        {
          "label": "the_output",
          "output_name": "out_file1"
        }
      ]
    }
  },
  "report": {
    "markdown": 42
  }
}

Interoperable (Declarative) Tests

Interoperable tests are YAML-driven expectation files in gxformat2/examples/expectations/. Unlike conventional Python tests, these are language-agnostic — the same expectation files drive both the Python test suite (via pytest) and can be consumed by TypeScript or other implementations. Each file contains named test cases specifying a fixture, an operation, and a list of path-based assertions against the result.

test_to_native_basic_structure:
  fixture: synthetic-basic.gxwf.yml
  operation: to_native
  assertions:
    - path: [a_galaxy_workflow]
      value: "true"
    - path: [steps, "1", tool_id]
      value: cat1
    - path: [steps, "1", workflow_outputs, $length]
      value: 1

Path elements:

Element	Meaning
str	Dict key lookup (falls back to attribute access)
int	List index
$length	Terminal — returns len(current)
{field: value}	Find first list item where item.field == value

Assertion modes:

Key	Check
value	Exact equality (None, str, int, list, dict)
value_contains	Substring containment
value_any_contains	Any element in a list contains the substring
value_set	Unordered set comparison (for frozenset properties like unique_tools)

Available operations:

• Normalization: normalized_format2, normalized_native, expanded_format2, expanded_native

• Conversion: to_format2, to_native, ensure_format2, ensure_native

• Validation: validate_format2, validate_format2_strict, validate_native, validate_native_strict

• Linting: lint_format2, lint_native — return {errors, warnings, error_count, warn_count}

• Best practices: lint_best_practices_format2, lint_best_practices_native — same return shape

Special keys:

• assertions may be omitted or empty — the operation succeeding is the test

• expect_error: true — the operation must raise; test passes on error, fails on success

# Positive: operation succeeds, no assertions needed
test_basic_valid_format2:
  fixture: synthetic-basic.gxwf.yml
  operation: validate_format2_strict

# Negative: operation must fail
test_extra_field_rejected:
  fixture: synthetic-extra-field.gxwf.yml
  operation: validate_format2_strict
  expect_error: true

The Python test runner (tests/test_interop_tests.py) parametrizes all cases and runs them via pytest.

Expectation Files

cytoscape.yml

Source on GitHub

Test	Fixture	Operation
test_simple_graph_emits_two_nodes_one_edge	synthetic-graph-simple.gxwf.yml	cytoscape_elements_to_list
test_simple_graph_input_node_shape	synthetic-graph-simple.gxwf.yml	cytoscape_elements_to_list
test_simple_graph_tool_step_shape	synthetic-graph-simple.gxwf.yml	cytoscape_elements_to_list
test_simple_graph_edge_shape	synthetic-graph-simple.gxwf.yml	cytoscape_elements_to_list
test_int_input_step_type	synthetic-int-input.gxwf.yml	cytoscape_node_ids
test_int_input_carries_int_step_type	synthetic-int-input.gxwf.yml	cytoscape_elements_to_list
test_subworkflow_step_classes	synthetic-graph-with-subworkflow.gxwf.yml	cytoscape_elements_to_list
test_subworkflow_edges	synthetic-graph-with-subworkflow.gxwf.yml	cytoscape_edge_ids
test_subworkflow_edge_named_output	synthetic-graph-with-subworkflow.gxwf.yml	cytoscape_elements_to_list
test_multi_data_inputs_distinct_ids	synthetic-multi-data-input.gxwf.yml	cytoscape_node_ids
test_multi_data_inputs_two_edges	synthetic-multi-data-input.gxwf.yml	cytoscape_edge_ids
test_real_hacked_unicycler_repo_link_populated	real-hacked-unicycler-assembly-extra-annotations.ga	cytoscape_elements_to_list
test_real_sars_cov2_smoke	real-sars-cov2-variant-calling.ga	cytoscape_node_ids

ensure_format2.yml

Source on GitHub

Test	Fixture	Operation
test_ensure_format2_converts_native	synthetic-labeled-tool.ga	ensure_format2
test_ensure_format2_normalizes_format2	synthetic-basic.gxwf.yml	ensure_format2

ensure_native.yml

Source on GitHub

Test	Fixture	Operation
test_ensure_native_converts_format2	synthetic-basic.gxwf.yml	ensure_native
test_ensure_native_normalizes_native	synthetic-minimal-tool.ga	ensure_native

lint_best_practices_format2.yml

Source on GitHub

Test	Fixture	Operation
test_bp_format2_clean	synthetic-basic.gxwf.yml	lint_best_practices_format2
test_bp_format2_no_annotation	synthetic-bp-no-annotation.gxwf.yml	lint_best_practices_format2
test_bp_format2_no_creator	synthetic-basic.gxwf.yml	lint_best_practices_format2
test_bp_format2_no_license	synthetic-basic.gxwf.yml	lint_best_practices_format2
test_bp_format2_disconnected_input	synthetic-bp-disconnected-input.gxwf.yml	lint_best_practices_format2
test_bp_format2_step_no_label	synthetic-bp-step-no-label.gxwf.yml	lint_best_practices_format2

lint_best_practices_native.yml

Source on GitHub

Test	Fixture	Operation
test_bp_native_no_annotation	synthetic-minimal-tool.ga	lint_best_practices_native
test_bp_native_no_creator	synthetic-minimal-tool.ga	lint_best_practices_native
test_bp_native_no_license	synthetic-minimal-tool.ga	lint_best_practices_native
test_bp_native_step_no_label	synthetic-minimal-tool.ga	lint_best_practices_native
test_bp_native_bad_creator_id	synthetic-unlinted-best-practices-bad-identifier.ga	lint_best_practices_native
test_bp_native_untyped_param	synthetic-unlinted-best-practices.ga	lint_best_practices_native
test_bp_native_disconnected_input	synthetic-unlinted-best-practices.ga	lint_best_practices_native
test_bp_native_untyped_pja	synthetic-unlinted-best-practices.ga	lint_best_practices_native

lint_format2.yml

Source on GitHub

Test	Fixture	Operation
test_lint_basic_clean	synthetic-basic.gxwf.yml	lint_format2
test_lint_nested_subworkflow_clean	synthetic-nested-subworkflow.gxwf.yml	lint_format2
test_lint_pja_clean	synthetic-pja-hide-rename.gxwf.yml	lint_format2
test_lint_tags_clean	synthetic-tags.gxwf.yml	lint_format2
test_lint_rules_tool_clean	synthetic-rules-tool.gxwf.yml	lint_format2
test_lint_runtime_inputs_clean	synthetic-runtime-inputs.gxwf.yml	lint_format2
test_lint_user_defined_tool_clean	synthetic-user-defined-tool.gxwf.yml	lint_format2
test_lint_slash_labels_clean	synthetic-slash-in-label-chained.gxwf.yml	lint_format2
test_lint_when_step_clean	synthetic-when-step.gxwf.yml	lint_format2
test_lint_float_default_clean	synthetic-float-input-default.gxwf.yml	lint_format2
test_lint_format2_missing_class	synthetic-lint-no-class.gxwf.yml	lint_format2
test_lint_format2_missing_steps	synthetic-missing-steps.gxwf.yml	lint_format2
test_lint_format2_nested_no_steps	synthetic-lint-nested-no-steps.gxwf.yml	lint_format2
test_lint_format2_step_errors	synthetic-lint-step-errors.gxwf.yml	lint_format2
test_lint_format2_testtoolshed	synthetic-lint-testtoolshed.gxwf.yml	lint_format2
test_lint_format2_bad_output_source	synthetic-lint-bad-output-source.gxwf.yml	lint_format2
test_lint_format2_bad_int_default	synthetic-lint-bad-int-default.gxwf.yml	lint_format2
test_lint_format2_bad_float_default	synthetic-lint-bad-float-default.gxwf.yml	lint_format2
test_lint_format2_bad_string_default	synthetic-lint-bad-string-default.gxwf.yml	lint_format2
test_lint_format2_report_clean	synthetic-lint-report.gxwf.yml	lint_format2

lint_native.yml

Source on GitHub

Test	Fixture	Operation
test_lint_native_unicycler_clean	real-unicycler-assembly.ga	lint_native
test_lint_native_no_outputs_warns	real-shed-tools-raw.ga	lint_native
test_lint_native_missing_tool_warns	real-hacked-unicycler-assembly-no-tool.ga	lint_native
test_lint_native_testtoolshed_warns	real-hacked-unicycler-assembly-testtoolshed.ga	lint_native
test_lint_native_minimal_no_outputs	synthetic-minimal-tool.ga	lint_native
test_lint_native_missing_steps	synthetic-lint-no-steps.ga	lint_native
test_lint_native_bad_format_version	synthetic-lint-bad-format-version.ga	lint_native
test_lint_native_bad_marker	synthetic-lint-bad-marker.ga	lint_native
test_lint_native_non_integer_step_key	synthetic-lint-non-integer-step.ga	lint_native
test_lint_native_nested_no_steps	synthetic-lint-nested-no-steps.ga	lint_native
test_lint_native_output_no_label	synthetic-lint-output-no-label.ga	lint_native
test_lint_native_missing_marker	synthetic-missing-marker.ga	lint_native
test_lint_native_report_clean	synthetic-lint-report.ga	lint_native

mermaid.yml

Source on GitHub

Test	Fixture	Operation
test_simple_graph_header	synthetic-graph-simple.gxwf.yml	workflow_to_mermaid_lines
test_simple_graph_data_input_shape	synthetic-graph-simple.gxwf.yml	workflow_to_mermaid_lines
test_simple_graph_tool_step_shape	synthetic-graph-simple.gxwf.yml	workflow_to_mermaid_lines
test_simple_graph_edge	synthetic-graph-simple.gxwf.yml	workflow_to_mermaid_lines
test_simple_graph_exact	synthetic-graph-simple.gxwf.yml	workflow_to_mermaid
test_multi_data_inputs_distinct_ids	synthetic-multi-data-input.gxwf.yml	workflow_to_mermaid_lines
test_int_input_renders	synthetic-int-input.gxwf.yml	workflow_to_mermaid_lines
test_subworkflow_step_uses_double_bracket_shape	synthetic-graph-with-subworkflow.gxwf.yml	workflow_to_mermaid_lines
test_frame_comments_ignored_by_default	synthetic-comments-dict.gxwf.yml	workflow_to_mermaid
test_frame_comments_not_emitted_without_flag	synthetic-comments-dict.gxwf.yml	workflow_to_mermaid
test_frame_comments_rendered_as_subgraph	synthetic-comments-dict.gxwf.yml	workflow_to_mermaid_with_comments_lines
test_basic_workflow_single_edge	synthetic-basic.gxwf.yml	workflow_to_mermaid_lines
test_real_sars_cov2_shape	real-sars-cov2-variant-calling.ga	workflow_to_mermaid_lines

normalized_comments.yml

Source on GitHub

Test	Fixture	Operation
test_comments_dict_to_list	synthetic-comments-dict.gxwf.yml	normalized_format2
test_comments_list_preserved	synthetic-comments-list.gxwf.yml	normalized_format2

normalized_format2.yml

Source on GitHub

Test	Fixture	Operation
test_simple_graph_extracts_main	synthetic-graph-simple.gxwf.yml	normalized_format2
test_graph_inlines_subworkflow_ref	synthetic-graph-with-subworkflow.gxwf.yml	normalized_format2
test_input_shorthand_expanded	synthetic-input-shorthand.gxwf.yml	normalized_format2
test_step_in_shorthand_expanded	synthetic-step-in-shorthand.gxwf.yml	normalized_format2
test_url_run_passes_through	synthetic-url-run-yml.gxwf.yml	normalized_format2
test_steps_without_run_unchanged	synthetic-step-in-shorthand.gxwf.yml	expanded_format2
test_inline_subworkflow_expanded	synthetic-outer-inline-subworkflow.ga	expanded_native
test_doc_array_joined	synthetic-doc-array.gxwf.yml	normalized_format2
test_input_type_alias_data_input	synthetic-input-type-aliases.gxwf.yml	normalized_format2
test_input_type_alias_file	synthetic-basic.gxwf.yml	normalized_format2
test_step_out_shorthand_expanded	synthetic-step-out-shorthand.gxwf.yml	normalized_format2
test_outputs_dict_to_list	synthetic-basic.gxwf.yml	normalized_format2
test_inputs_array_form	synthetic-inputs-array.gxwf.yml	normalized_format2
test_tool_state_json_parsed	synthetic-tool-state-json.gxwf.yml	normalized_format2
test_tags_present	synthetic-tags.gxwf.yml	normalized_format2
test_link_resolved_to_connected_value	synthetic-nested-subworkflow.gxwf.yml	normalized_format2
test_int_link_coerced_to_str	synthetic-int-link.gxwf.yml	normalized_format2
test_multisource_bare_list	synthetic-multisource-bare-list.gxwf.yml	normalized_format2

normalized_inputs.yml

Source on GitHub

Test	Fixture	Operation
test_optional_input_flag	synthetic-optional-input.gxwf.yml	normalized_format2
test_integer_type_alias	synthetic-integer-type-alias.gxwf.yml	normalized_format2
test_float_type_and_default	synthetic-float-input-default.gxwf.yml	normalized_format2
test_string_type_and_default	synthetic-string-input.gxwf.yml	normalized_format2
test_paired_list_collection_type	synthetic-paired-list-input.gxwf.yml	normalized_format2
test_record_collection_type_and_fields	synthetic-record-input.gxwf.yml	normalized_format2
test_record_fields_round_trip_to_native	synthetic-record-input.gxwf.yml	to_native
test_sample_sheet_collection_type	synthetic-sample-sheet-input.gxwf.yml	normalized_format2
test_multi_data_input_sources	synthetic-multi-data-input.gxwf.yml	normalized_format2
test_multi_string_input_type	synthetic-multi-string-input.gxwf.yml	normalized_format2

normalized_labels.yml

Source on GitHub

Test	Fixture	Operation
test_slash_in_input_label_normalized	synthetic-slash-in-input-label.gxwf.yml	normalized_format2
test_slash_in_step_label_normalized	synthetic-slash-in-step-label.gxwf.yml	normalized_format2
test_slash_in_label_chained_connection	synthetic-slash-in-label-chained.gxwf.yml	normalized_format2
test_slash_in_input_label_to_native	synthetic-slash-in-input-label.gxwf.yml	to_native
test_slash_in_label_chained_to_native	synthetic-slash-in-label-chained.gxwf.yml	to_native

normalized_native.yml

Source on GitHub

Test	Fixture	Operation
test_tool_state_always_dict	synthetic-minimal-tool.ga	normalized_native
test_containers_never_none	synthetic-minimal-tool.ga	normalized_native
test_tags_never_none	synthetic-minimal-tool.ga	normalized_native
test_connected_paths_empty	synthetic-minimal-tool.ga	normalized_native
test_extra_position_fields_stripped	synthetic-unlinted-best-practices.ga	normalized_native

normalized_steps.yml

Source on GitHub

Test	Fixture	Operation
test_when_expression	synthetic-when-step.gxwf.yml	normalized_format2
test_pja_hide_and_rename	synthetic-pja-hide-rename.gxwf.yml	normalized_format2
test_runtime_inputs	synthetic-runtime-inputs.gxwf.yml	normalized_format2
test_rules_tool_link_resolution	synthetic-rules-tool.gxwf.yml	normalized_format2
test_user_defined_tool_run	synthetic-user-defined-tool.gxwf.yml	normalized_format2
test_pipe_separated_input_key	synthetic-string-input.gxwf.yml	normalized_format2

post_job_actions.yml

Source on GitHub

Test	Fixture	Operation
test_step_post_job_actions_normalized	synthetic-step-post-job-actions.gxwf.yml	normalized_format2
test_step_post_job_actions_to_native	synthetic-step-post-job-actions.gxwf.yml	to_native
test_step_post_job_actions_round_trip	synthetic-step-post-job-actions.gxwf.yml	ensure_native
test_step_post_job_actions_merged_with_out_shorthand	synthetic-step-post-job-actions-merged.gxwf.yml	to_native

to_format2.yml

Source on GitHub

Test	Fixture	Operation
test_to_format2_metadata	synthetic-labeled-tool.ga	to_format2
test_to_format2_inputs	synthetic-labeled-tool.ga	to_format2
test_to_format2_outputs	synthetic-labeled-tool.ga	to_format2
test_to_format2_tool_step	synthetic-labeled-tool.ga	to_format2
test_to_format2_step_inputs	synthetic-labeled-tool.ga	to_format2
test_to_format2_inline_subworkflow	synthetic-outer-inline-subworkflow.ga	to_format2
test_to_format2_url_subworkflow	synthetic-outer-url-subworkflow.ga	to_format2
test_to_format2_rename_pja	synthetic-rename-pja.ga	to_format2

to_native.yml

Source on GitHub

Test	Fixture	Operation
test_to_native_basic_structure	synthetic-basic.gxwf.yml	to_native
test_to_native_input_step_type	synthetic-basic.gxwf.yml	to_native
test_to_native_tool_step	synthetic-basic.gxwf.yml	to_native
test_to_native_tool_connections	synthetic-basic.gxwf.yml	to_native
test_to_native_workflow_outputs	synthetic-basic.gxwf.yml	to_native
test_to_native_int_input	synthetic-int-input.gxwf.yml	to_native
test_to_native_inline_subworkflow	synthetic-graph-with-subworkflow.gxwf.yml	to_native
test_to_native_url_subworkflow	synthetic-url-run-yml.gxwf.yml	to_native
test_to_native_pause_step	synthetic-pause-step.gxwf.yml	to_native
test_to_native_comments	synthetic-comments-list.gxwf.yml	to_native
test_to_native_when_expression	synthetic-when-step.gxwf.yml	to_native
test_to_native_pja_hide	synthetic-pja-hide-rename.gxwf.yml	to_native
test_to_native_pja_rename	synthetic-pja-hide-rename.gxwf.yml	to_native
test_to_native_multi_data_connections	synthetic-multi-data-input.gxwf.yml	to_native
test_to_native_user_defined_tool	synthetic-user-defined-tool.gxwf.yml	to_native
test_to_native_comments_dict	synthetic-comments-dict.gxwf.yml	to_native
test_to_native_step_input_default_scalar	synthetic-step-input-default-scalar.gxwf.yml	to_native
test_to_native_step_input_default_file	synthetic-step-input-default-file.gxwf.yml	to_native

unique_tools.yml

Source on GitHub

Test	Fixture	Operation
test_single_tool_format2	synthetic-single-versioned-tool.gxwf.yml	normalized_format2
test_no_tool_steps_format2	synthetic-input-shorthand.gxwf.yml	normalized_format2
test_null_tool_version	synthetic-step-in-shorthand.gxwf.yml	normalized_format2
test_inline_subworkflow_format2	synthetic-tool-with-inline-subworkflow.gxwf.yml	normalized_format2
test_single_tool_native	synthetic-minimal-tool.ga	normalized_native
test_no_tool_steps_native	synthetic-native-data-input.ga	normalized_native
test_inline_subworkflow_native	synthetic-native-tool-with-subworkflow.ga	normalized_native

validate_format2.yml

Source on GitHub

Test	Fixture	Operation
test_basic_valid_format2	synthetic-basic.gxwf.yml	validate_format2
test_basic_valid_format2_strict	synthetic-basic.gxwf.yml	validate_format2_strict
test_extra_field_valid_format2_lax	synthetic-extra-field.gxwf.yml	validate_format2
test_extra_field_rejected_format2_strict	synthetic-extra-field.gxwf.yml	validate_format2_strict
test_missing_steps_rejected_format2	synthetic-missing-steps.gxwf.yml	validate_format2
test_missing_steps_rejected_format2_strict	synthetic-missing-steps.gxwf.yml	validate_format2_strict
test_nested_subworkflow_valid_format2	synthetic-nested-subworkflow.gxwf.yml	validate_format2
test_nested_subworkflow_valid_format2_strict	synthetic-nested-subworkflow.gxwf.yml	validate_format2_strict
test_unlinted_best_practices_rejected_format2	synthetic-unlinted-best-practices.gxwf.yml	validate_format2
test_unlinted_best_practices_rejected_format2_strict	synthetic-unlinted-best-practices.gxwf.yml	validate_format2_strict
test_inner_subworkflow_valid_format2	synthetic-inner-subworkflow.gxwf.yml	validate_format2
test_inner_subworkflow_valid_format2_strict	synthetic-inner-subworkflow.gxwf.yml	validate_format2_strict
test_input_shorthand_valid_format2	synthetic-input-shorthand.gxwf.yml	validate_format2
test_input_shorthand_valid_format2_strict	synthetic-input-shorthand.gxwf.yml	validate_format2_strict
test_step_in_shorthand_valid_format2	synthetic-step-in-shorthand.gxwf.yml	validate_format2
test_step_in_shorthand_valid_format2_strict	synthetic-step-in-shorthand.gxwf.yml	validate_format2_strict
test_url_run_yml_valid_format2	synthetic-url-run-yml.gxwf.yml	validate_format2
test_url_run_yml_valid_format2_strict	synthetic-url-run-yml.gxwf.yml	validate_format2_strict
test_inner_nested_subworkflow_valid_format2	synthetic-inner-nested-subworkflow.gxwf.yml	validate_format2
test_inner_nested_subworkflow_valid_format2_strict	synthetic-inner-nested-subworkflow.gxwf.yml	validate_format2_strict
test_single_versioned_tool_valid_format2	synthetic-single-versioned-tool.gxwf.yml	validate_format2
test_single_versioned_tool_valid_format2_strict	synthetic-single-versioned-tool.gxwf.yml	validate_format2_strict
test_tool_with_inline_subworkflow_valid_format2	synthetic-tool-with-inline-subworkflow.gxwf.yml	validate_format2
test_tool_with_inline_subworkflow_valid_format2_strict	synthetic-tool-with-inline-subworkflow.gxwf.yml	validate_format2_strict
test_int_input_valid_format2	synthetic-int-input.gxwf.yml	validate_format2
test_int_input_valid_format2_strict	synthetic-int-input.gxwf.yml	validate_format2_strict
test_pause_step_valid_format2	synthetic-pause-step.gxwf.yml	validate_format2
test_pause_step_valid_format2_strict	synthetic-pause-step.gxwf.yml	validate_format2_strict
test_comments_list_valid_format2	synthetic-comments-list.gxwf.yml	validate_format2
test_comments_list_valid_format2_strict	synthetic-comments-list.gxwf.yml	validate_format2_strict
test_doc_array_valid_format2	synthetic-doc-array.gxwf.yml	validate_format2
test_doc_array_valid_format2_strict	synthetic-doc-array.gxwf.yml	validate_format2_strict
test_input_type_aliases_valid_format2	synthetic-input-type-aliases.gxwf.yml	validate_format2
test_input_type_aliases_valid_format2_strict	synthetic-input-type-aliases.gxwf.yml	validate_format2_strict
test_step_out_shorthand_valid_format2	synthetic-step-out-shorthand.gxwf.yml	validate_format2
test_step_out_shorthand_valid_format2_strict	synthetic-step-out-shorthand.gxwf.yml	validate_format2_strict
test_inputs_array_valid_format2	synthetic-inputs-array.gxwf.yml	validate_format2
test_inputs_array_valid_format2_strict	synthetic-inputs-array.gxwf.yml	validate_format2_strict
test_tool_state_json_valid_format2	synthetic-tool-state-json.gxwf.yml	validate_format2
test_tool_state_json_valid_format2_strict	synthetic-tool-state-json.gxwf.yml	validate_format2_strict
test_tags_valid_format2	synthetic-tags.gxwf.yml	validate_format2
test_tags_valid_format2_strict	synthetic-tags.gxwf.yml	validate_format2_strict
test_optional_input_valid_format2	synthetic-optional-input.gxwf.yml	validate_format2
test_optional_input_valid_format2_strict	synthetic-optional-input.gxwf.yml	validate_format2_strict
test_when_step_valid_format2	synthetic-when-step.gxwf.yml	validate_format2
test_when_step_valid_format2_strict	synthetic-when-step.gxwf.yml	validate_format2_strict
test_pja_hide_rename_valid_format2	synthetic-pja-hide-rename.gxwf.yml	validate_format2
test_pja_hide_rename_valid_format2_strict	synthetic-pja-hide-rename.gxwf.yml	validate_format2_strict
test_paired_list_input_valid_format2	synthetic-paired-list-input.gxwf.yml	validate_format2
test_paired_list_input_valid_format2_strict	synthetic-paired-list-input.gxwf.yml	validate_format2_strict
test_float_input_default_valid_format2	synthetic-float-input-default.gxwf.yml	validate_format2
test_float_input_default_valid_format2_strict	synthetic-float-input-default.gxwf.yml	validate_format2_strict
test_string_input_valid_format2	synthetic-string-input.gxwf.yml	validate_format2
test_string_input_valid_format2_strict	synthetic-string-input.gxwf.yml	validate_format2_strict
test_integer_type_alias_valid_format2	synthetic-integer-type-alias.gxwf.yml	validate_format2
test_integer_type_alias_valid_format2_strict	synthetic-integer-type-alias.gxwf.yml	validate_format2_strict
test_multi_data_input_valid_format2	synthetic-multi-data-input.gxwf.yml	validate_format2
test_multi_data_input_valid_format2_strict	synthetic-multi-data-input.gxwf.yml	validate_format2_strict
test_multi_string_input_valid_format2	synthetic-multi-string-input.gxwf.yml	validate_format2
test_multi_string_input_valid_format2_strict	synthetic-multi-string-input.gxwf.yml	validate_format2_strict
test_rules_tool_valid_format2	synthetic-rules-tool.gxwf.yml	validate_format2
test_rules_tool_valid_format2_strict	synthetic-rules-tool.gxwf.yml	validate_format2_strict
test_runtime_inputs_valid_format2	synthetic-runtime-inputs.gxwf.yml	validate_format2
test_runtime_inputs_valid_format2_strict	synthetic-runtime-inputs.gxwf.yml	validate_format2_strict
test_slash_in_input_label_valid_format2	synthetic-slash-in-input-label.gxwf.yml	validate_format2
test_slash_in_input_label_valid_format2_strict	synthetic-slash-in-input-label.gxwf.yml	validate_format2_strict
test_slash_in_step_label_valid_format2	synthetic-slash-in-step-label.gxwf.yml	validate_format2
test_slash_in_step_label_valid_format2_strict	synthetic-slash-in-step-label.gxwf.yml	validate_format2_strict
test_slash_in_label_chained_valid_format2	synthetic-slash-in-label-chained.gxwf.yml	validate_format2
test_slash_in_label_chained_valid_format2_strict	synthetic-slash-in-label-chained.gxwf.yml	validate_format2_strict
test_sample_sheet_input_valid_format2	synthetic-sample-sheet-input.gxwf.yml	validate_format2
test_sample_sheet_input_valid_format2_strict	synthetic-sample-sheet-input.gxwf.yml	validate_format2_strict
test_text_restrictions_valid_format2	synthetic-text-restrictions.gxwf.yml	validate_format2
test_text_restrictions_valid_format2_strict	synthetic-text-restrictions.gxwf.yml	validate_format2_strict
test_text_restrictions_options_valid_format2	synthetic-text-restrictions-options.gxwf.yml	validate_format2
test_text_restrictions_options_valid_format2_strict	synthetic-text-restrictions-options.gxwf.yml	validate_format2_strict
test_text_suggestions_valid_format2	synthetic-text-suggestions.gxwf.yml	validate_format2
test_text_suggestions_valid_format2_strict	synthetic-text-suggestions.gxwf.yml	validate_format2_strict
test_text_restrict_on_connections_valid_format2	synthetic-text-restrict-on-connections.gxwf.yml	validate_format2
test_text_restrict_on_connections_valid_format2_strict	synthetic-text-restrict-on-connections.gxwf.yml	validate_format2_strict
test_restrictions_on_data_rejected_format2	synthetic-bad-restrictions-on-data.gxwf.yml	validate_format2
test_restrictions_on_data_rejected_format2_strict	synthetic-bad-restrictions-on-data.gxwf.yml	validate_format2_strict
test_column_defs_on_list_rejected_format2	synthetic-bad-column-defs-on-list.gxwf.yml	validate_format2
test_column_defs_on_list_rejected_format2_strict	synthetic-bad-column-defs-on-list.gxwf.yml	validate_format2_strict
test_column_default_mismatch_rejected_format2	synthetic-bad-column-default-mismatch.gxwf.yml	validate_format2
test_column_default_mismatch_rejected_format2_strict	synthetic-bad-column-default-mismatch.gxwf.yml	validate_format2_strict
test_record_input_valid_format2	synthetic-record-input.gxwf.yml	validate_format2
test_record_input_valid_format2_strict	synthetic-record-input.gxwf.yml	validate_format2_strict
test_fields_on_list_rejected_format2	synthetic-bad-fields-on-list.gxwf.yml	validate_format2
test_fields_on_list_rejected_format2_strict	synthetic-bad-fields-on-list.gxwf.yml	validate_format2_strict
test_comments_dict_valid_format2	synthetic-comments-dict.gxwf.yml	validate_format2
test_comments_dict_valid_format2_strict	synthetic-comments-dict.gxwf.yml	validate_format2_strict
test_user_defined_tool_valid_format2	synthetic-user-defined-tool.gxwf.yml	validate_format2
test_user_defined_tool_valid_format2_strict	synthetic-user-defined-tool.gxwf.yml	validate_format2_strict
test_report_bad_type_rejected_format2	synthetic-lint-report-bad-type.gxwf.yml	validate_format2
test_report_bad_type_rejected_format2_strict	synthetic-lint-report-bad-type.gxwf.yml	validate_format2_strict

validate_native.yml

Source on GitHub

Test	Fixture	Operation
test_minimal_valid_native	synthetic-minimal-tool.ga	validate_native
test_minimal_valid_native_strict	synthetic-minimal-tool.ga	validate_native_strict
test_extra_field_valid_native_lax	synthetic-extra-field.ga	validate_native
test_extra_field_rejected_native_strict	synthetic-extra-field.ga	validate_native_strict
test_missing_marker_rejected_native	synthetic-missing-marker.ga	validate_native
test_missing_marker_rejected_native_strict	synthetic-missing-marker.ga	validate_native_strict
test_unicycler_assembly_valid_native	real-unicycler-assembly.ga	validate_native
test_unicycler_assembly_valid_native_strict	real-unicycler-assembly.ga	validate_native_strict
test_unicycler_assembly_with_tags_valid_native	real-hacked-unicycler-assembly-with-tags.ga	validate_native
test_unicycler_assembly_with_tags_valid_native_strict	real-hacked-unicycler-assembly-with-tags.ga	validate_native_strict
test_unicycler_assembly_no_tool_valid_native	real-hacked-unicycler-assembly-no-tool.ga	validate_native
test_unicycler_assembly_no_tool_valid_native_strict	real-hacked-unicycler-assembly-no-tool.ga	validate_native_strict
test_unicycler_assembly_testtoolshed_valid_native	real-hacked-unicycler-assembly-testtoolshed.ga	validate_native
test_unicycler_assembly_testtoolshed_valid_native_strict	real-hacked-unicycler-assembly-testtoolshed.ga	validate_native_strict
test_unicycler_assembly_extra_annotations_valid_native	real-hacked-unicycler-assembly-extra-annotations.ga	validate_native
test_unicycler_assembly_extra_annotations_valid_native_strict	real-hacked-unicycler-assembly-extra-annotations.ga	validate_native_strict
test_sars_cov2_variant_calling_rejected_native	real-sars-cov2-variant-calling.ga	validate_native
test_sars_cov2_variant_calling_rejected_native_strict	real-sars-cov2-variant-calling.ga	validate_native_strict
test_ecoli_comparison_valid_native	real-ecoli-comparison.ga	validate_native
test_ecoli_comparison_valid_native_strict	real-ecoli-comparison.ga	validate_native_strict
test_shed_tools_raw_valid_native	real-shed-tools-raw.ga	validate_native
test_shed_tools_raw_valid_native_strict	real-shed-tools-raw.ga	validate_native_strict
test_multi_string_input_valid_native	real-multi-string-input.ga	validate_native
test_multi_string_input_valid_native_strict	real-multi-string-input.ga	validate_native_strict
test_basic_without_step_input_label_valid_native	real-basic-without-step-input-label.ga	validate_native
test_basic_without_step_input_label_valid_native_strict	real-basic-without-step-input-label.ga	validate_native_strict
test_unlinted_best_practices_valid_native	synthetic-unlinted-best-practices.ga	validate_native
test_unlinted_best_practices_rejected_native_strict	synthetic-unlinted-best-practices.ga	validate_native_strict
test_unlinted_best_practices_dict_tool_state_valid_native	synthetic-unlinted-best-practices-dict-tool-state.ga	validate_native
test_unlinted_best_practices_dict_tool_state_rejected_native_strict	synthetic-unlinted-best-practices-dict-tool-state.ga	validate_native_strict
test_unlinted_best_practices_bad_identifier_valid_native	synthetic-unlinted-best-practices-bad-identifier.ga	validate_native
test_unlinted_best_practices_bad_identifier_rejected_native_strict	synthetic-unlinted-best-practices-bad-identifier.ga	validate_native_strict
test_inner_subworkflow_valid_native	synthetic-inner-subworkflow.ga	validate_native
test_inner_subworkflow_valid_native_strict	synthetic-inner-subworkflow.ga	validate_native_strict
test_native_data_input_valid_native	synthetic-native-data-input.ga	validate_native
test_native_data_input_valid_native_strict	synthetic-native-data-input.ga	validate_native_strict
test_outer_inline_subworkflow_valid_native	synthetic-outer-inline-subworkflow.ga	validate_native
test_outer_inline_subworkflow_valid_native_strict	synthetic-outer-inline-subworkflow.ga	validate_native_strict
test_outer_url_subworkflow_valid_native	synthetic-outer-url-subworkflow.ga	validate_native
test_outer_url_subworkflow_valid_native_strict	synthetic-outer-url-subworkflow.ga	validate_native_strict
test_native_tool_with_subworkflow_valid_native	synthetic-native-tool-with-subworkflow.ga	validate_native
test_native_tool_with_subworkflow_valid_native_strict	synthetic-native-tool-with-subworkflow.ga	validate_native_strict
test_labeled_tool_valid_native	synthetic-labeled-tool.ga	validate_native
test_labeled_tool_valid_native_strict	synthetic-labeled-tool.ga	validate_native_strict
test_rename_pja_valid_native	synthetic-rename-pja.ga	validate_native
test_rename_pja_valid_native_strict	synthetic-rename-pja.ga	validate_native_strict
test_report_bad_type_rejected_native	synthetic-lint-report-bad-type.ga	validate_native
test_report_bad_type_rejected_native_strict	synthetic-lint-report-bad-type.ga	validate_native_strict
test_bad_marker_rejected_native	synthetic-lint-bad-marker.ga	validate_native
test_bad_marker_rejected_native_strict	synthetic-lint-bad-marker.ga	validate_native_strict
test_bad_format_version_rejected_native	synthetic-lint-bad-format-version.ga	validate_native
test_bad_format_version_rejected_native_strict	synthetic-lint-bad-format-version.ga	validate_native_strict