Mercurial > repos > shellac > sam_consensus_v3
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/galaxy/util/rules_dsl_spec.yml Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,485 @@ +- 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