annotate env/lib/python3.9/site-packages/galaxy/util/rules_dsl_spec.yml @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

- doc: add_column_basename functions properly on absolute and relative paths
  rules:
    - type: add_column_basename
      target_column: 0
  initial:
    data: [['/path/to/moo.txt'], ['moo.txt']]
    sources: [1, 2]
  final:
    data:
      - [/path/to/moo.txt, moo.txt]
      - [moo.txt, moo.txt]
- doc: add_column_regex works with simple captures by default
  rules:
    - type: add_column_regex
      target_column: 0
      expression: '(o)+'
  initial:
    data: [[foo], [cow]]
    sources: [1,2]
  final:
    data: [[foo, oo], [cow, o]]
- doc: add_column_regex works with replacements if supplied
  rules:
    - type: add_column_regex
      target_column: 0
      expression: '(o+)'
      replacement: 'the os \1'
  initial:
    data: [[foo], [cow]]
    sources: [1,2]
  final:
    data: [["foo", "the os oo"], ["cow", "the os o"]]
- doc: add_column_regex works with multiple groups when group_count specified
  rules:
    - type: add_column_regex
      target_column: 0
      expression: '.*(o)(o)'
      group_count: 2
  initial:
    data: [[foo], [boo]]
    sources: [1,2]
  final:
    data: [["foo", "o", "o"], ["boo", "o", "o"]]
- doc: add_column_substr works for keeping a fixed length prefix
  rules:
    - type: add_column_substr
      target_column: 0
      substr_type: keep_prefix
      length: 2
  initial:
    data: [[foo], [cow], [ba], [d]]
    sources: [1, 2]
  final:
    data: [[foo, fo], [cow, co], [ba, ba], [d, d]]
- doc: add_column_substr works for keeping a fixed length suffix
  rules:
    - type: add_column_substr
      target_column: 0
      substr_type: keep_suffix
      length: 2
  initial:
    data: [[foo], [cow], [ba], [d]]
    sources: [1, 2]
  final:
    data: [[foo, oo], [cow, ow], [ba, ba], [d, d]]
- doc: add_column_substr works for dropping a fixed length prefix
  rules:
    - type: add_column_substr
      target_column: 0
      substr_type: drop_prefix
      length: 2
  initial:
    data: [[foo], [cow], [ba], [d]]
    sources: [1, 2]
  final:
    data: [[foo, o], [cow, w], [ba, ""], [d, ""]]
- doc: add_column_substr works for dropping a fixed length suffix
  rules:
    - type: add_column_substr
      target_column: 0
      substr_type: drop_suffix
      length: 2
  initial:
    data: [[foo], [cow], [ba], [d]]
    sources: [1, 2]
  final:
    data: [[foo, f], [cow, c], [ba, ""], [d, ""]]
- rules:
    - type: add_column_rownum
      start: 1
  initial:
    data: [[foo], [cow], [ba], [d]]
    sources: [1, 2, 3, 4]
  final:
    data: [[foo, "1"], [cow, "2"], [ba, "3"], [d, "4"]]
- rules:
    - type: add_column_rownum
      start: 0
  initial:
    data: [[foo], [cow], [ba], [d]]
    sources: [1, 2, 3, 4]
  final:
    data: [[foo, "0"], [cow, "1"], [ba, "2"], [d, "3"]]
- rules:
    - type: add_column_value
      value: "moo"
  initial:
    data: [[foo], [cow]]
    sources: [1, 2]
  final:
    data: [[foo, moo], [cow, moo]]
- rules:
    - type: remove_columns
      target_columns: [0, 1]
  initial:
    data: [[a, b, c], [e, f, g]]
    sources: [1, 2]
  final:
    data: [[c], [g]]
- rules:
    - type: remove_columns
      target_columns: [2]
  initial:
    data: [[a, b, c], [e, f, g]]
    sources: [1, 2]
  final:
    data: [[a, b], [e, f]]
- rules:
    - type: add_filter_regex
      target_column: 0
      expression: '(a+)'
      invert: false
  initial:
    data: [[a, b, c], [e, f, g]]
    sources: [1, 2]
  final:
    data: [[a, b, c]]
- rules:
    - type: add_filter_regex
      target_column: 2
      expression: '(c+)'
      invert: true
  initial:
    data: [[a, b, c], [e, f, g]]
    sources: [1, 2]
  final:
    data: [[e, f, g]]
    sources: [2]
- rules:
    - type: add_filter_count
      count: 1
      which: first
      invert: false
  initial:
    data: [[a, b, c], [e, f, g], [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[e, f, g], [h, i, j]]
    sources: [2, 3]
- rules:
    - type: add_filter_count
      count: 0
      which: first
      invert: false
  initial:
    data: [[a, b, c], [e, f, g], [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[a, b, c], [e, f, g], [h, i, j]]
    sources: [1, 2, 3]
- rules:
    - type: add_filter_count
      count: 1
      which: last
      invert: false
  initial:
    data: [[a, b, c], [e, f, g], [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[a, b, c], [e, f, g]]
    sources: [1, 2]
- rules:
    - type: add_filter_count
      count: 1
      which: last
      invert: true
  initial:
    data: [[a, b, c], [e, f, g], [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[h, i, j]]
    sources: [3]
- rules:
   - type: add_filter_empty
     target_column: 0
     invert: false
  initial:
    data: [["", "b", "c"], ["a", "b", "c"]]
    sources: [1, 2]
  final:
    data: [["a", "b", "c"]]
    sources: [2]
- rules:
   - type: add_filter_empty
     target_column: 0
     invert: true
  initial:
    data: [["", "b", "c"], ["a", "b", "c"]]
    sources: [moo, cow]
  final:
    data: [["", "b", "c"]]
    sources: [moo]

- rules:
    - type: add_filter_matches
      value: a
      target_column: 0
      invert: false
  initial:
    data: [[a, b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[a, b, c]]
    sources: [1]

- rules:
    - type: add_filter_matches
      value: a
      target_column: 0
      invert: true
  initial:
    data: [[a, b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[e, f, g],
           [h, i, j]]
    sources: [2, 3]

- rules:
    - type: add_filter_matches
      value: p
      target_column: 1
      invert: false
  initial:
    data: [[a, b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: []
    sources: []

- rules:
    - type: add_filter_matches
      value: a
      target_column: 1
      invert: false
  initial:
    data: [['a ', b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: []
    sources: []

- rules:
    - type: add_filter_matches
      value: 'a '
      target_column: 1
      invert: false
  initial:
    data: [[a, b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: []
    sources: []

- rules:
    - type: add_filter_matches
      value: p
      target_column: 1
      invert: true
  initial:
    data: [[a, b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]
  final:
    data: [[a, b, c],
           [e, f, g],
           [h, i, j]]
    sources: [1, 2, 3]

- rules:
    - type: add_filter_compare
      target_column: 0
      value: 13
      compare_type: less_than
  initial:
    data: [["1", "moo"], ["10", "cow"], ["13", "rat"], ["20", "dog"], ["30", "cat"]]
    sources: [1, 2, 3, 4, 5]
  final:
    data: [["1", "moo"], ["10", "cow"]]
    sources: [1, 2]

- rules:
    - type: add_filter_compare
      target_column: 0
      value: 13
      compare_type: less_than_equal
  initial:
    data: [["1", "moo"], ["10", "cow"], ["13", "rat"], ["20", "dog"], ["30", "cat"]]
    sources: [1, 2, 3, 4, 5]
  final:
    data: [["1", "moo"], ["10", "cow"], ["13", "rat"]]
    sources: [1, 2, 3]

- rules:
    - type: add_filter_compare
      target_column: 0
      value: 13
      compare_type: greater_than
  initial:
    data: [["1", "moo"], ["10", "cow"], ["13", "rat"], ["20", "dog"], ["30", "cat"]]
    sources: [1, 2, 3, 4, 5]
  final:
    data: [["20", "dog"], ["30", "cat"]]
    sources: [4, 5]

- rules:
    - type: add_filter_compare
      target_column: 0
      value: 13
      compare_type: greater_than_equal
  initial:
    data: [["1", "moo"], ["10", "cow"], ["13", "rat"], ["20", "dog"], ["30", "cat"]]
    sources: [1, 2, 3, 4, 5]
  final:
    data: [["13", "rat"], ["20", "dog"], ["30", "cat"]]
    sources: [3, 4, 5]

- rules:
    - type: sort
      numeric: false
      target_column: 0
  initial:
    data: [["moo", "cow"], ["meow", "cat"], ["bark", "dog"]]
    sources: [1, 2, 3]
  final:
    data: [["bark", "dog"], ["meow", "cat"], ["moo", "cow"]]
    sources: [3, 2, 1]

- rules:
    - type: sort
      numeric: false
      target_column: 1
  initial:
    data: [["moo", "cow"], ["meow", "cat"], ["bark", "dog"]]
    sources: [1, 2, 3]
  final:
    data: [["meow", "cat"], ["moo", "cow"], ["bark", "dog"]]
    sources: [2, 1, 3]

- rules:
    - type: sort
      numeric: false
      target_column: 1
  initial:
    data: [["moo", "cow"], ["meow", "cat"], ["bark", "Dog"]]
    sources: [1, 2, 3]
  final:
    data: [["bark", "Dog"], ["meow", "cat"], ["moo", "cow"]]
    sources: [3, 2, 1]

- rules:
    - type: swap_columns
      target_column_0: 0
      target_column_1: 1
  initial:
    data: [["moo", "cow"], ["meow", "cat"], ["bark", "Dog"]]
    sources: [1, 2, 3]
  final:
    data: [["cow", "moo"], ["cat", "meow"], ["Dog", "bark"]]
    sources: [1, 2, 3]

- rules:
    - type: split_columns
      target_columns_0: [0]
      target_columns_1: [1]
  initial:
    data: [["moo", "cow", "A"], ["meow", "cat", "B"], ["bark", "Dog", "C"]]
    sources: [1, 2, 3]
  final:
    data: [["moo", "A"], ["cow", "A"], ["meow", "B"], ["cat", "B"], ["bark", "C"], ["Dog", "C"]]
    sources: [1, 1, 2, 2, 3, 3]

- rules:
    - type: add_column_metadata
      value: identifier0
  initial:
    data: [["moo"], ["meow"], ["bark"]]
    sources: [{"identifiers": ["cow"]}, {"identifiers": ["cat"]}, {"identifiers": ["dog"]}]
  final:
    data: [["moo", "cow"], ["meow", "cat"], ["bark", "dog"]]

- rules:
    - type: add_column_metadata
      value: tags
  initial:
    data: [["moo"], ["meow"], ["bark"]]
    sources: [{"identifiers": ["cow"], "tags": ["farm"]}, {"identifiers": ["cat"], "tags": ["house"]}, {"identifiers": ["dog"], "tags": ["house", "firestation"]}]
  final:
    data: [["moo", "farm"], ["meow", "house"], ["bark", "firestation,house"]]

- rules:
    - type: add_column_group_tag_value
      value: where
      default_value: ''
  initial:
    data: [["moo"], ["meow"], ["bark"]]
    sources: [{"identifiers": ["cow"], "tags": ["group:where:farm"]}, {"identifiers": ["cat"], "tags": ["group:where:house"]}, {"identifiers": ["dog"], "tags": ["group:where:house"]}]
  final:
    data: [["moo", "farm"], ["meow", "house"], ["bark", "house"]]

- doc: add_column_group_tag_value uses default value
  rules:
    - type: add_column_group_tag_value
      value: where
      default_value: 'barn'
  initial:
    data: [["moo"], ["meow"], ["bark"]]
    sources: [{"identifiers": ["cow"], "tags": []}, {"identifiers": ["cat"], "tags": ["group:where:house"]}, {"identifiers": ["dog"], "tags": ["group:where:firestation"]}]
  final:
    data: [["moo", "barn"], ["meow", "house"], ["bark", "firestation"]]

- doc: add_column_group_tag_value sorts and grabs first tag value if multiple present
  rules:
    - type: add_column_group_tag_value
      value: where
      default_value: 'barn'
  initial:
    data: [["moo"], ["meow"], ["bark"]]
    sources: [{"identifiers": ["cow"], "tags": []}, {"identifiers": ["cat"], "tags": ["group:where:house", "group:where:kittenpile"]}, {"identifiers": ["dog"], "tags": ["group:where:house", "group:where:firestation"]}]
  final:
    data: [["moo", "barn"], ["meow", "house"], ["bark", "firestation"]]

- rules:
    - type: invalid_rule_type
  error: true

- rules:
    - type: add_filter_compare
      target_column: 0
      value: 13
      compare_type: invalid_compare_type
  error: true

- rules:
    - type: add_column_concatenate
      target_column: 0
  error: true

- rules:
    - type: add_column_basename
      target_column_0: 0
  error: true

- rules:
    - type: add_column_regex
      target_column: 0
      regex: '(o)+'
  error: true

- rules:
    - type: add_column_regex
      target_column: 0
      expression: '(o+'
  error: true