diff gmql_syntax.yaml @ 0:a80c93182db3 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gmql_syntax.yaml	Tue Jun 26 09:08:06 2018 -0400
@@ -0,0 +1,89 @@
+---
+GMQL-VERSION: 'V2.1'
+STATEMENT:
+    '{out_var} = {operator} ({parameters}) {in_vars};'
+MATERIALIZE:
+    'MATERIALIZE {variable} INTO {file_name};'
+PARAMS:
+    type_separator: '; '
+    param_separator: ', '
+    wff:
+        NOT: 'NOT ({p})'
+        AND: '{p1} AND {p2}'
+        OR: '{p1} OR  {p2}'
+        BLOCK: '({p})'
+    predicate:
+        eq: '{att} == {val}'
+        lt: '{att} < {val}'
+        gt: '{att} > {val}'
+        let: '{att} <= {val}'
+        get: '{att} >= {val}'
+        values:
+            string: "'{p}'"
+            float: "{p}"
+            int: "{p}"
+            coordinate: "{p}"
+            meta: "META({p})"
+    metajoin_condition:
+        SIMPLE: '{att_name}'
+        FULL: 'FULL({att_name})'
+        EXACT: 'EXACT({att_name})'
+    new_region: '{r} AS {function}'
+    function: '{function}({arg})'
+    SELECT:
+        metadata: '{predicate}'
+        region: 'region: {predicate}'
+        semijoin: 'semijoin: {predicate}'
+        semijoin_predicates:
+            IN: '{attributes} IN {ds_ext}'
+            NOT_IN: '{attributes} NOT IN {ds_ext}'
+    PROJECT:
+        regions: '{att_list}'
+        metadata: 'metadata: {att_list}'
+        att_list:
+            keep: '{att_list}'
+            exclude: 'ALLBUT {att_list}'
+        newRegions: 'region_update: {newAttributes}'
+        newMetadata: 'metadata_update: {newAttributes}'
+    MAP:
+        regions: '{newRegions}'
+        count: 'count_name: {count_name}'
+        joinby: 'joinby: {joinbyClause}'
+    COVER:
+        groupby: 'groupby: {groupbyClause}'
+        regions: 'aggregate: {newRegions}'
+    EXTEND: ''
+    GROUP:
+        meta: '{groupMeta}'
+        newMetadata: 'meta_aggregates: {newAttributes}'
+        regions: 'region_keys: {groupRegions}'
+        newRegions: 'region_aggregates: {newRegions}'
+    MERGE:
+        groupby: 'groupby: {groupbyClause}'
+    UNION: ''
+    DIFFERENCE:
+        exact: 'exact: {flag}'
+        joinby: 'joinby: {joinbyClause}'
+    ORDER:
+        att_list:
+            asc: '{att}'
+            desc: '{att} DESC'
+        metadata:
+            orderingAttributes: '{att_list}'
+            top:
+                n: 'meta_top: {k}'
+                perc: 'meta_topp: {k}'
+                group: 'meta_topg: {k}'
+        region:
+            orderingAttributes: 'region_order: {att_list}'
+            top:
+                n: 'region_top: {k}'
+                perc: 'region_topp: {k}'
+                group: 'region_topg: {k}'
+    JOIN:
+        genomic_predicate: '{genomic_predicate}'
+        equi_clause: 'on_attributes: {att_list}'
+        output_opt: 'output: {coord_param}'
+        joinby: 'joinby: {joinbyClause}'
+        distal_condition: '{dc}({n})'
+        distal_stream: '{ds}'
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