Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/galaxy/util/rules_dsl_spec.yml @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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- 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