@nfdi4plants/arctrl 3.0.0-beta.14 → 3.0.0-beta.16

package/dist/ts/ts/CWL/Decode.js

@@ -1,13 +1,13 @@
-import { getEnumerator, disposeSafe } from '../../node_modules/@fable-org/fable-library-js/Util.js';
-import { YAMLElement_Sequence } from '../fable_modules/YAMLicious.0.0.3/YAMLiciousTypes.fs.js';
+import { getEnumerator, disposeSafe, Lazy } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { YAMLElement_Sequence } from '../fable_modules/YAMLicious.1.0.0-alpha.2/YAMLiciousTypes.fs.js';
 import { setProperty, setOptionalProperty } from '../fable_modules/DynamicObj.7.1.0/DynObj.fs.js';
 import { DynamicObj } from '../fable_modules/DynamicObj.7.1.0/DynamicObj.fs.js';
-import { isEmpty, head, tail, iterate, map, empty, ofArray } from '../../node_modules/@fable-org/fable-library-js/List.js';
-import { object, string, bool, map as map$1, resizearray, float, int, read } from '../fable_modules/YAMLicious.0.0.3/Decode.fs.js';
+import { isEmpty, head, tail, iterate, map, empty, exists, ofArray, singleton as singleton$1, tryHead } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { object, string, bool, resizearray, map as map$1, float, int, read } from '../fable_modules/YAMLicious.1.0.0-alpha.2/Decode.fs.js';
 import { toFail, printf, toText, replace } from '../../node_modules/@fable-org/fable-library-js/String.js';
 import { OutputBinding, CWLOutput } from './Outputs.js';
 import { value, some } from '../../node_modules/@fable-org/fable-library-js/Option.js';
-import { CWLType_Dirent, DirentInstance, CWLType_Array, CWLType_Boolean, CWLType_Double, CWLType_Float, CWLType_Long, CWLType_Int, CWLType_String, CWLType_Directory, DirectoryInstance_$ctor, CWLType_File, FileInstance_$ctor, CWLType_Stdout, CWLType_Null, SoftwarePackage, SchemaDefRequirementType_$ctor_541DA560 } from './CWLTypes.js';
+import { CWLType_Dirent, DirentInstance, InputArraySchema, InputRecordField, InputRecordSchema, InputEnumSchema, CWLType_Null, CWLType_Stdout, CWLType_Boolean, CWLType_Double, CWLType_Float, CWLType_Long, CWLType_Int, CWLType_String, CWLType_Directory, DirectoryInstance_$ctor, CWLType_File, FileInstance_$ctor, CWLType_Array, CWLType_Union, CWLType_Record, CWLType_Enum, SoftwarePackage, SchemaDefRequirementType_$ctor_541DA560 } from './CWLTypes.js';
 import { toArray, delay, collect, append, empty as empty$1, singleton, item, length, map as map$2 } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
 import { getItemFromDict } from '../../node_modules/@fable-org/fable-library-js/MapUtil.js';
 import { FSharpMap__get_Keys, FSharpMap__get_Values } from '../../node_modules/@fable-org/fable-library-js/Map.js';
@@ -183,41 +183,239 @@ const Decode_direntDecoder = (value_1) => object((get$) => {
   let objectArg, objectArg_1, objectArg_2;
   return CWLType_Dirent(new DirentInstance((objectArg = get$.Required, objectArg.Field("entry", Decode_decodeStringOrExpression)), (objectArg_1 = get$.Optional, objectArg_1.Field("entryname", Decode_decodeStringOrExpression)), (objectArg_2 = get$.Optional, objectArg_2.Field("writable", bool))));
 }, value_1);
-const Decode_cwlArrayTypeDecoder = (value_1) => object((get$) => {
-  let objectArg_1;
-  let items;
-  const objectArg = get$.Required;
-  items = objectArg.Field("items", string);
-  switch (items) {
+function inputArraySchemaDecoder$004090() {
+  return (value_3) => object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3;
+    return new InputArraySchema(Decode_cwlTypeDecoder$0027((objectArg = get$.Required, objectArg.Field("items", (x) => x))), (objectArg_1 = get$.Optional, objectArg_1.Field("label", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", string)));
+  }, value_3);
+}
+const inputArraySchemaDecoder$004090$002D1 = new Lazy(inputArraySchemaDecoder$004090);
+function inputRecordFieldDecoder$0040104() {
+  return (value_3) => object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3;
+    return new InputRecordField((objectArg = get$.Required, objectArg.Field("name", string)), Decode_cwlTypeDecoder$0027((objectArg_1 = get$.Required, objectArg_1.Field("type", (x) => x))), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("label", string)));
+  }, value_3);
+}
+const inputRecordFieldDecoder$0040104$002D1 = new Lazy(inputRecordFieldDecoder$0040104);
+function inputRecordSchemaDecoder$0040121() {
+  return (value_4) => object((get$) => {
+    let fields, enumerator, objectArg_1, objectArg_2, objectArg_3;
+    let fieldsDict;
+    const objectArg = get$.Optional;
+    fieldsDict = objectArg.Field("fields", (value) => object((get2) => get2.Overflow.FieldList(empty()), value));
+    return new InputRecordSchema(fieldsDict == null ? void 0 : (fields = [], enumerator = getEnumerator(value(fieldsDict)), (() => {
+      try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+          const kvp = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+          const fieldType = Decode_cwlTypeDecoder$0027(kvp[1]);
+          void fields.push(new InputRecordField(kvp[0], fieldType, void 0, void 0));
+        }
+      } finally {
+        disposeSafe(enumerator);
+      }
+    })(), fields), (objectArg_1 = get$.Optional, objectArg_1.Field("label", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", string)));
+  }, value_4);
+}
+const inputRecordSchemaDecoder$0040121$002D1 = new Lazy(inputRecordSchemaDecoder$0040121);
+function inputEnumSchemaDecoder$0040154() {
+  return (value_5) => object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3;
+    return new InputEnumSchema((objectArg = get$.Required, objectArg.Field("symbols", (value) => resizearray(string, value))), (objectArg_1 = get$.Optional, objectArg_1.Field("label", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", string)));
+  }, value_5);
+}
+const inputEnumSchemaDecoder$0040154$002D1 = new Lazy(inputEnumSchemaDecoder$0040154);
+function Decode_cwlSimpleTypeFromString(s) {
+  switch (s) {
     case "File":
-      return CWLType_Array(CWLType_File(FileInstance_$ctor()));
+      return CWLType_File(FileInstance_$ctor());
     case "Directory":
-      return CWLType_Array(CWLType_Directory(DirectoryInstance_$ctor()));
-    case "Dirent":
-      return CWLType_Array((objectArg_1 = get$.Required, objectArg_1.Field("listing", Decode_direntDecoder)));
+      return CWLType_Directory(DirectoryInstance_$ctor());
     case "string":
-      return CWLType_Array(CWLType_String());
+      return CWLType_String();
     case "int":
-      return CWLType_Array(CWLType_Int());
+      return CWLType_Int();
     case "long":
-      return CWLType_Array(CWLType_Long());
+      return CWLType_Long();
     case "float":
-      return CWLType_Array(CWLType_Float());
+      return CWLType_Float();
     case "double":
-      return CWLType_Array(CWLType_Double());
+      return CWLType_Double();
     case "boolean":
-      return CWLType_Array(CWLType_Boolean());
+      return CWLType_Boolean();
+    case "stdout":
+      return CWLType_Stdout();
+    case "null":
+      return CWLType_Null();
     default:
-      throw new Error("Invalid CWL type");
+      throw new Error(`Invalid CWL simple type: ${s}`);
   }
-}, value_1);
+}
+const Decode_inputArraySchemaDecoder = inputArraySchemaDecoder$004090$002D1.Value;
+const Decode_inputRecordFieldDecoder = inputRecordFieldDecoder$0040104$002D1.Value;
+const Decode_inputRecordSchemaDecoder = inputRecordSchemaDecoder$0040121$002D1.Value;
+const Decode_inputEnumSchemaDecoder = inputEnumSchemaDecoder$0040154$002D1.Value;
+function Decode_cwlTypeDecoder$0027(element) {
+  let collection;
+  const parseTypeString = (typeStr) => {
+    const patternInput = typeStr.endsWith("?") ? [replace(typeStr, "?", ""), true] : [typeStr, false];
+    const stripped = patternInput[0];
+    const baseType_1 = stripped.endsWith("[]") ? CWLType_Array(new InputArraySchema(Decode_cwlSimpleTypeFromString(replace(stripped, "[]", "")), void 0, void 0, void 0)) : Decode_cwlSimpleTypeFromString(stripped);
+    if (patternInput[1]) {
+      return CWLType_Union([CWLType_Null(), baseType_1]);
+    } else {
+      return baseType_1;
+    }
+  };
+  let matchResult, v, items;
+  switch (element.tag) {
+    case /* Value */
+    1: {
+      matchResult = 0;
+      v = element.fields[0];
+      break;
+    }
+    case /* Object */
+    3: {
+      if (!isEmpty(element.fields[0])) {
+        if (head(element.fields[0]).tag === /* Value */
+        1) {
+          if (isEmpty(tail(element.fields[0]))) {
+            matchResult = 0;
+            v = head(element.fields[0]).fields[0];
+          } else {
+            matchResult = 2;
+          }
+        } else {
+          matchResult = 2;
+        }
+      } else {
+        matchResult = 2;
+      }
+      break;
+    }
+    case /* Sequence */
+    2: {
+      matchResult = 1;
+      items = element.fields[0];
+      break;
+    }
+    default:
+      matchResult = 3;
+  }
+  switch (matchResult) {
+    case 0:
+      return parseTypeString(v.Value);
+    case 1:
+      return CWLType_Union((collection = map(Decode_cwlTypeDecoder$0027, items), Array.from(collection)));
+    case 2:
+      return object((get$) => {
+        let objectArg_1;
+        let typeField;
+        const objectArg = get$.Optional;
+        typeField = objectArg.Field("type", (x) => x);
+        let matchResult_1, v_1;
+        if (typeField != null) {
+          if (value(typeField).tag === /* Object */
+          3) {
+            if (!isEmpty(value(typeField).fields[0])) {
+              if (head(value(typeField).fields[0]).tag === /* Value */
+              1) {
+                if (isEmpty(tail(value(typeField).fields[0]))) {
+                  matchResult_1 = 0;
+                  v_1 = head(value(typeField).fields[0]).fields[0];
+                } else {
+                  matchResult_1 = 1;
+                }
+              } else {
+                matchResult_1 = 1;
+              }
+            } else {
+              matchResult_1 = 1;
+            }
+          } else {
+            matchResult_1 = 2;
+          }
+        } else {
+          matchResult_1 = 2;
+        }
+        switch (matchResult_1) {
+          case 0: {
+            const matchValue = v_1.Value;
+            return matchValue === "record" ? CWLType_Record(inputRecordSchemaDecoder$0040121$002D1.Value(element)) : matchValue === "enum" ? CWLType_Enum(inputEnumSchemaDecoder$0040154$002D1.Value(element)) : matchValue === "array" ? CWLType_Array(inputArraySchemaDecoder$004090$002D1.Value(element)) : parseTypeString(matchValue);
+          }
+          case 1:
+            return Decode_cwlTypeDecoder$0027((objectArg_1 = get$.Required, objectArg_1.Field("type", (x_1) => x_1)));
+          default:
+            throw new Error("Unexpected type format in cwlTypeDecoder'");
+        }
+      }, element);
+    default:
+      throw new Error("Unexpected YAMLElement in cwlTypeDecoder'");
+  }
+}
 function Decode_cwlTypeStringMatcher(t, get$) {
-  let objectArg, objectArg_1;
+  let objectArg;
   const patternInput = t.endsWith("?") ? [true, replace(t, "?", "")] : [false, t];
+  const optional = patternInput[0];
   const newT = patternInput[1];
-  return [newT === "File" ? CWLType_File(FileInstance_$ctor()) : newT === "Directory" ? CWLType_Directory(DirectoryInstance_$ctor()) : newT === "Dirent" ? (objectArg = get$.Required, objectArg.Field("listing", Decode_direntDecoder)) : newT === "string" ? CWLType_String() : newT === "int" ? CWLType_Int() : newT === "long" ? CWLType_Long() : newT === "float" ? CWLType_Float() : newT === "double" ? CWLType_Double() : newT === "boolean" ? CWLType_Boolean() : newT === "File[]" ? CWLType_Array(CWLType_File(FileInstance_$ctor())) : newT === "Directory[]" ? CWLType_Array(CWLType_Directory(DirectoryInstance_$ctor())) : newT === "Dirent[]" ? CWLType_Array((objectArg_1 = get$.Required, objectArg_1.Field("listing", Decode_direntDecoder))) : newT === "string[]" ? CWLType_Array(CWLType_String()) : newT === "int[]" ? CWLType_Array(CWLType_Int()) : newT === "long[]" ? CWLType_Array(CWLType_Long()) : newT === "float[]" ? CWLType_Array(CWLType_Float()) : newT === "double[]" ? CWLType_Array(CWLType_Double()) : newT === "boolean[]" ? CWLType_Array(CWLType_Boolean()) : newT === "stdout" ? CWLType_Stdout() : newT === "null" ? CWLType_Null() : (() => {
-    throw new Error("Invalid CWL type");
-  })(), patternInput[0]];
+  let cwlType;
+  if (newT.endsWith("[]")) {
+    const baseType = replace(newT, "[]", "");
+    cwlType = CWLType_Array(new InputArraySchema(baseType === "File" ? CWLType_File(FileInstance_$ctor()) : baseType === "Directory" ? CWLType_Directory(DirectoryInstance_$ctor()) : baseType === "Dirent" ? (objectArg = get$.Required, objectArg.Field("listing", Decode_direntDecoder)) : baseType === "string" ? CWLType_String() : baseType === "int" ? CWLType_Int() : baseType === "long" ? CWLType_Long() : baseType === "float" ? CWLType_Float() : baseType === "double" ? CWLType_Double() : baseType === "boolean" ? CWLType_Boolean() : (() => {
+      throw new Error("Invalid CWL type");
+    })(), void 0, void 0, void 0));
+  } else {
+    switch (newT) {
+      case "File": {
+        cwlType = CWLType_File(FileInstance_$ctor());
+        break;
+      }
+      case "Directory": {
+        cwlType = CWLType_Directory(DirectoryInstance_$ctor());
+        break;
+      }
+      case "Dirent": {
+        const objectArg_1 = get$.Required;
+        cwlType = objectArg_1.Field("listing", Decode_direntDecoder);
+        break;
+      }
+      case "string": {
+        cwlType = CWLType_String();
+        break;
+      }
+      case "int": {
+        cwlType = CWLType_Int();
+        break;
+      }
+      case "long": {
+        cwlType = CWLType_Long();
+        break;
+      }
+      case "float": {
+        cwlType = CWLType_Float();
+        break;
+      }
+      case "double": {
+        cwlType = CWLType_Double();
+        break;
+      }
+      case "boolean": {
+        cwlType = CWLType_Boolean();
+        break;
+      }
+      case "stdout": {
+        cwlType = CWLType_Stdout();
+        break;
+      }
+      case "null": {
+        cwlType = CWLType_Null();
+        break;
+      }
+      default:
+        throw new Error("Invalid CWL type");
+    }
+  }
+  return [optional ? CWLType_Union([CWLType_Null(), cwlType]) : cwlType, optional];
 }
 const Decode_cwlTypeDecoder = (value_1) => object((get$) => {
   let objectArg_1;
@@ -267,7 +465,7 @@ const Decode_cwlTypeDecoder = (value_1) => object((get$) => {
     }
   });
   if (cwlType == null) {
-    return [(objectArg_1 = get$.Required, objectArg_1.Field("type", Decode_cwlArrayTypeDecoder)), false];
+    return [(objectArg_1 = get$.Required, objectArg_1.Field("type", Decode_cwlTypeDecoder$0027)), false];
   } else {
     return Decode_cwlTypeStringMatcher(value(cwlType), get$);
   }
@@ -383,14 +581,98 @@ const Decode_inputBindingDecoder = (value_5) => object((get$) => {
 const Decode_inputArrayDecoder = (value_1) => object((get$) => {
   const dict = get$.Overflow.FieldList(empty());
   const collection = toArray(delay(() => collect((key) => {
-    let v;
     const value = getItemFromDict(dict, key);
     const inputBinding = Decode_inputBindingDecoder(value);
-    const patternInput = value.tag === /* Object */
-    3 ? !isEmpty(value.fields[0]) ? head(value.fields[0]).tag === /* Value */
-    1 ? isEmpty(tail(value.fields[0])) ? (v = head(value.fields[0]).fields[0], Decode_cwlTypeStringMatcher(v.Value, get$)) : Decode_cwlTypeDecoder(value) : Decode_cwlTypeDecoder(value) : Decode_cwlTypeDecoder(value) : Decode_cwlTypeDecoder(value);
+    let patternInput;
+    let matchResult, v, mappings;
+    if (value.tag === /* Object */
+    3) {
+      if (!isEmpty(value.fields[0])) {
+        if (head(value.fields[0]).tag === /* Value */
+        1) {
+          if (isEmpty(tail(value.fields[0]))) {
+            matchResult = 0;
+            v = head(value.fields[0]).fields[0];
+          } else {
+            matchResult = 1;
+            mappings = value.fields[0];
+          }
+        } else {
+          matchResult = 1;
+          mappings = value.fields[0];
+        }
+      } else {
+        matchResult = 1;
+        mappings = value.fields[0];
+      }
+    } else {
+      matchResult = 2;
+    }
+    switch (matchResult) {
+      case 0: {
+        patternInput = Decode_cwlTypeStringMatcher(v.Value, get$);
+        break;
+      }
+      case 1: {
+        if (exists((m) => {
+          let matchResult_1, k_1;
+          if (m.tag === /* Mapping */
+          0) {
+            if (m.fields[0].Value === "type") {
+              matchResult_1 = 0;
+              k_1 = m.fields[0];
+            } else {
+              matchResult_1 = 1;
+            }
+          } else {
+            matchResult_1 = 1;
+          }
+          switch (matchResult_1) {
+            case 0:
+              return true;
+            default:
+              return false;
+          }
+        }, mappings)) {
+          patternInput = Decode_cwlTypeDecoder(value);
+        } else {
+          let matchResult_2, v_1;
+          if (value.tag === /* Object */
+          3) {
+            if (!isEmpty(value.fields[0])) {
+              if (head(value.fields[0]).tag === /* Value */
+              1) {
+                if (isEmpty(tail(value.fields[0]))) {
+                  matchResult_2 = 0;
+                  v_1 = head(value.fields[0]).fields[0];
+                } else {
+                  matchResult_2 = 1;
+                }
+              } else {
+                matchResult_2 = 1;
+              }
+            } else {
+              matchResult_2 = 1;
+            }
+          } else {
+            matchResult_2 = 1;
+          }
+          switch (matchResult_2) {
+            case 0: {
+              patternInput = Decode_cwlTypeStringMatcher(v_1.Value, get$);
+              break;
+            }
+            default:
+              throw new Error("Unexpected input format without type field");
+          }
+        }
+        break;
+      }
+      default:
+        throw new Error("Unexpected input format in inputArrayDecoder");
+    }
     const input = new CWLInput(key, patternInput[0]);
-    return append(inputBinding != null ? (setOptionalProperty("inputBinding", inputBinding, input), empty$1()) : empty$1(), delay(() => append(patternInput[1] ? (setOptionalProperty("optional", true, input), empty$1()) : empty$1(), delay(() => singleton(input)))));
+    return append(patternInput[1] ? (setOptionalProperty("optional", true, input), empty$1()) : empty$1(), delay(() => append(inputBinding != null ? (setOptionalProperty("inputBinding", inputBinding, input), empty$1()) : empty$1(), delay(() => singleton(input)))));
   }, dict.keys())));
   return Array.from(collection);
 }, value_1);
@@ -399,8 +681,76 @@ const Decode_inputsDecoder = (value) => object((get$) => {
   return objectArg.Field("inputs", Decode_inputArrayDecoder);
 }, value);
 const Decode_baseCommandDecoder = (value_2) => object((get$) => {
+  let baseCommandField;
   const objectArg = get$.Optional;
-  return objectArg.Field("baseCommand", (value) => resizearray(string, value));
+  baseCommandField = objectArg.Field("baseCommand", (x) => x);
+  let matchResult, v, v_1, s, s_1;
+  if (baseCommandField == null) {
+    matchResult = 4;
+  } else {
+    switch (value(baseCommandField).tag) {
+      case /* Object */
+      3: {
+        if (!isEmpty(value(baseCommandField).fields[0])) {
+          switch (head(value(baseCommandField).fields[0]).tag) {
+            case /* Value */
+            1: {
+              if (isEmpty(tail(value(baseCommandField).fields[0]))) {
+                matchResult = 0;
+                v = head(value(baseCommandField).fields[0]).fields[0];
+              } else {
+                matchResult = 5;
+              }
+              break;
+            }
+            case /* Sequence */
+            2: {
+              if (isEmpty(tail(value(baseCommandField).fields[0]))) {
+                matchResult = 2;
+                s = head(value(baseCommandField).fields[0]).fields[0];
+              } else {
+                matchResult = 5;
+              }
+              break;
+            }
+            default:
+              matchResult = 5;
+          }
+        } else {
+          matchResult = 5;
+        }
+        break;
+      }
+      case /* Value */
+      1: {
+        matchResult = 1;
+        v_1 = value(baseCommandField).fields[0];
+        break;
+      }
+      case /* Sequence */
+      2: {
+        matchResult = 3;
+        s_1 = value(baseCommandField).fields[0];
+        break;
+      }
+      default:
+        matchResult = 5;
+    }
+  }
+  switch (matchResult) {
+    case 0:
+      return [v.Value];
+    case 1:
+      return [v_1.Value];
+    case 2:
+      return resizearray(string, YAMLElement_Sequence(s));
+    case 3:
+      return resizearray(string, YAMLElement_Sequence(s_1));
+    case 4:
+      return void 0;
+    default:
+      return void 0;
+  }
 }, value_2);
 const Decode_versionDecoder = (value_1) => object((get$) => {
   const objectArg = get$.Required;
@@ -422,6 +772,79 @@ function Decode_stringFieldDecoder(field) {
     return objectArg.Field(field, string);
   }, value_1);
 }
+function Decode_sourceArrayFieldDecoder(field) {
+  return (value_2) => object((get$) => {
+    let sourceField;
+    const objectArg = get$.Optional;
+    sourceField = objectArg.Field(field, (x) => x);
+    if (sourceField == null) {
+      return void 0;
+    } else {
+      const sourceValue = value(sourceField);
+      let matchResult, v, v_1, s, s_1;
+      switch (sourceValue.tag) {
+        case /* Object */
+        3: {
+          if (!isEmpty(sourceValue.fields[0])) {
+            switch (head(sourceValue.fields[0]).tag) {
+              case /* Value */
+              1: {
+                if (isEmpty(tail(sourceValue.fields[0]))) {
+                  matchResult = 0;
+                  v = head(sourceValue.fields[0]).fields[0];
+                } else {
+                  matchResult = 4;
+                }
+                break;
+              }
+              case /* Sequence */
+              2: {
+                if (isEmpty(tail(sourceValue.fields[0]))) {
+                  matchResult = 2;
+                  s = head(sourceValue.fields[0]).fields[0];
+                } else {
+                  matchResult = 4;
+                }
+                break;
+              }
+              default:
+                matchResult = 4;
+            }
+          } else {
+            matchResult = 4;
+          }
+          break;
+        }
+        case /* Value */
+        1: {
+          matchResult = 1;
+          v_1 = sourceValue.fields[0];
+          break;
+        }
+        case /* Sequence */
+        2: {
+          matchResult = 3;
+          s_1 = sourceValue.fields[0];
+          break;
+        }
+        default:
+          matchResult = 4;
+      }
+      switch (matchResult) {
+        case 0:
+          return [v.Value];
+        case 1:
+          return [v_1.Value];
+        case 2:
+          return resizearray(string, YAMLElement_Sequence(s));
+        case 3:
+          return resizearray(string, YAMLElement_Sequence(s_1));
+        default:
+          return void 0;
+      }
+    }
+  }, value_2);
+}
 const Decode_inputStepDecoder = (value_1) => object((get$) => {
   const dict = get$.Overflow.FieldList(empty());
   const collection = toArray(delay(() => collect((key) => {
@@ -429,13 +852,91 @@ const Decode_inputStepDecoder = (value_1) => object((get$) => {
     const value$1 = getItemFromDict(dict, key);
     return singleton(new StepInput(key, (s1 = value$1.tag === /* Object */
     3 ? !isEmpty(value$1.fields[0]) ? head(value$1.fields[0]).tag === /* Value */
-    1 ? isEmpty(tail(value$1.fields[0])) ? (v = head(value$1.fields[0]).fields[0], v.Value) : void 0 : void 0 : void 0 : void 0, s2 = Decode_stringOptionFieldDecoder("source")(value$1), s1 != null ? value(s1) : s2 != null ? value(s2) : void 0), Decode_stringOptionFieldDecoder("default")(value$1), Decode_stringOptionFieldDecoder("valueFrom")(value$1)));
+    1 ? isEmpty(tail(value$1.fields[0])) ? (v = head(value$1.fields[0]).fields[0], [v.Value]) : void 0 : void 0 : void 0 : void 0, s2 = Decode_sourceArrayFieldDecoder("source")(value$1), s1 != null ? value(s1) : s2 != null ? value(s2) : void 0), Decode_stringOptionFieldDecoder("default")(value$1), Decode_stringOptionFieldDecoder("valueFrom")(value$1), Decode_stringOptionFieldDecoder("linkMerge")(value$1)));
   }, dict.keys())));
   return Array.from(collection);
 }, value_1);
 const Decode_outputStepsDecoder = (value_2) => object((get$) => {
-  const objectArg = get$.Required;
-  return objectArg.Field("out", (value) => resizearray(string, value));
+  let outField;
+  const objectArg = get$.Optional;
+  outField = objectArg.Field("out", (x) => x);
+  let matchResult, v_1, value$1;
+  if (outField == null) {
+    matchResult = 3;
+  } else {
+    switch (value(outField).tag) {
+      case /* Object */
+      3: {
+        if (!isEmpty(value(outField).fields[0])) {
+          switch (head(value(outField).fields[0]).tag) {
+            case /* Value */
+            1: {
+              if (isEmpty(tail(value(outField).fields[0]))) {
+                if (head(value(outField).fields[0]).fields[0].Value === "[]") {
+                  matchResult = 0;
+                  v_1 = head(value(outField).fields[0]).fields[0];
+                } else {
+                  matchResult = 2;
+                  value$1 = value(outField);
+                }
+              } else {
+                matchResult = 2;
+                value$1 = value(outField);
+              }
+              break;
+            }
+            case /* Sequence */
+            2: {
+              if (isEmpty(head(value(outField).fields[0]).fields[0])) {
+                if (isEmpty(tail(value(outField).fields[0]))) {
+                  matchResult = 1;
+                } else {
+                  matchResult = 2;
+                  value$1 = value(outField);
+                }
+              } else {
+                matchResult = 2;
+                value$1 = value(outField);
+              }
+              break;
+            }
+            default: {
+              matchResult = 2;
+              value$1 = value(outField);
+            }
+          }
+        } else {
+          matchResult = 2;
+          value$1 = value(outField);
+        }
+        break;
+      }
+      case /* Sequence */
+      2: {
+        if (isEmpty(value(outField).fields[0])) {
+          matchResult = 1;
+        } else {
+          matchResult = 2;
+          value$1 = value(outField);
+        }
+        break;
+      }
+      default: {
+        matchResult = 2;
+        value$1 = value(outField);
+      }
+    }
+  }
+  switch (matchResult) {
+    case 0:
+      return [];
+    case 1:
+      return [];
+    case 2:
+      return resizearray(string, value$1);
+    default:
+      return [];
+  }
 }, value_2);
 const Decode_stepArrayDecoder = (value_1) => object((get$) => {
   const dict = get$.Overflow.FieldList(empty());
@@ -454,6 +955,14 @@ const Decode_stepArrayDecoder = (value_1) => object((get$) => {
   }, dict.keys())));
   return Array.from(collection);
 }, value_1);
+const Decode_docDecoder = (value_1) => object((get$) => {
+  const objectArg = get$.Optional;
+  return objectArg.Field("doc", string);
+}, value_1);
+const Decode_labelDecoder = (value_1) => object((get$) => {
+  const objectArg = get$.Optional;
+  return objectArg.Field("label", string);
+}, value_1);
 const Decode_stepsDecoder = (value) => object((get$) => {
   const objectArg = get$.Required;
   return objectArg.Field("steps", Decode_stepArrayDecoder);
@@ -465,12 +974,14 @@ function Decode_commandLineToolDecoder(yamlCWL) {
   const requirements = Decode_requirementsDecoder(yamlCWL);
   const hints = Decode_hintsDecoder(yamlCWL);
   const baseCommand = Decode_baseCommandDecoder(yamlCWL);
+  const doc = Decode_docDecoder(yamlCWL);
+  const label = Decode_labelDecoder(yamlCWL);
   const description = new CWLToolDescription(outputs, cwlVersion);
   let metadata;
   const md = new DynamicObj();
   object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "class", "id", "label", "doc", "requirements", "hints", "cwlVersion", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
   metadata = md;
-  object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(ofArray(["id", "label", "doc", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
+  object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(ofArray(["id", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
   if (inputs != null) {
     description.Inputs = inputs;
   }
@@ -483,6 +994,12 @@ function Decode_commandLineToolDecoder(yamlCWL) {
   if (baseCommand != null) {
     description.BaseCommand = baseCommand;
   }
+  if (doc != null) {
+    description.Doc = doc;
+  }
+  if (label != null) {
+    description.Label = label;
+  }
   if (length(metadata.GetProperties(false)) > 0) {
     description.Metadata = metadata;
   }
@@ -503,18 +1020,27 @@ function Decode_workflowDecoder(yamlCWL) {
   }
   const requirements = Decode_requirementsDecoder(yamlCWL);
   const hints = Decode_hintsDecoder(yamlCWL);
-  const description = new CWLWorkflowDescription(Decode_stepsDecoder(yamlCWL), inputs, outputs, cwlVersion);
+  const steps = Decode_stepsDecoder(yamlCWL);
+  const doc = Decode_docDecoder(yamlCWL);
+  const label = Decode_labelDecoder(yamlCWL);
+  const description = new CWLWorkflowDescription(steps, inputs, outputs, cwlVersion);
   let metadata;
   const md = new DynamicObj();
-  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "class", "steps", "id", "label", "doc", "requirements", "hints", "cwlVersion"]))), yamlCWL);
+  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "label", "doc", "class", "steps", "id", "requirements", "hints", "cwlVersion"]))), yamlCWL);
   metadata = md;
-  object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(ofArray(["id", "label", "doc"]))), yamlCWL);
+  object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(singleton$1("id"))), yamlCWL);
   if (requirements != null) {
     description.Requirements = requirements;
   }
   if (hints != null) {
     description.Hints = hints;
   }
+  if (doc != null) {
+    description.Doc = doc;
+  }
+  if (label != null) {
+    description.Label = label;
+  }
   if (length(metadata.GetProperties(false)) > 0) {
     description.Metadata = metadata;
   }
@@ -536,6 +1062,7 @@ function Decode_decodeCWLProcessingUnit(cwl) {
   }
 }
 function DecodeParameters_cwlParameterReferenceDecoder(get$, key, yEle) {
+  let v_1;
   let matchResult, v, v1, v2, s;
   if (yEle.tag === /* Object */
   3) {
@@ -631,8 +1158,116 @@ function DecodeParameters_cwlParameterReferenceDecoder(get$, key, yEle) {
       return new CWLParameterReference(key, [v.Value]);
     case 1:
       return new CWLParameterReference(key, [v2.Value], Decode_cwlTypeStringMatcher(v1.Value, get$)[0]);
-    case 2:
-      return new CWLParameterReference(key, resizearray(string, YAMLElement_Sequence(s)));
+    case 2: {
+      const matchValue = tryHead(s);
+      let matchResult_1, mappings;
+      if (matchValue != null) {
+        if (value(matchValue).tag === /* Object */
+        3) {
+          matchResult_1 = 0;
+          mappings = value(matchValue).fields[0];
+        } else {
+          matchResult_1 = 1;
+        }
+      } else {
+        matchResult_1 = 1;
+      }
+      switch (matchResult_1) {
+        case 0:
+          if (!exists((_arg) => {
+            if (_arg.tag === /* Mapping */
+            0) {
+              return true;
+            } else {
+              return false;
+            }
+          }, mappings)) {
+            return new CWLParameterReference(key, resizearray(string, YAMLElement_Sequence(s)));
+          } else if (exists((_arg_1) => {
+            let matchResult_2, k_1;
+            if (_arg_1.tag === /* Mapping */
+            0) {
+              if (_arg_1.fields[0].Value === "class") {
+                matchResult_2 = 0;
+                k_1 = _arg_1.fields[0];
+              } else {
+                matchResult_2 = 1;
+              }
+            } else {
+              matchResult_2 = 1;
+            }
+            switch (matchResult_2) {
+              case 0:
+                return true;
+              default:
+                return false;
+            }
+          }, mappings)) {
+            const paths = [];
+            const enumerator = getEnumerator(s);
+            try {
+              while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const item = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                if (item.tag === /* Object */
+                3) {
+                  const enumerator_1 = getEnumerator(item.fields[0]);
+                  try {
+                    while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+                      const mapping = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                      let matchResult_3, k_3, v_2;
+                      if (mapping.tag === /* Mapping */
+                      0) {
+                        if (mapping.fields[1].tag === /* Object */
+                        3) {
+                          if (!isEmpty(mapping.fields[1].fields[0])) {
+                            if (head(mapping.fields[1].fields[0]).tag === /* Value */
+                            1) {
+                              if (isEmpty(tail(mapping.fields[1].fields[0]))) {
+                                if (v_1 = head(mapping.fields[1].fields[0]).fields[0], mapping.fields[0].Value === "path") {
+                                  matchResult_3 = 0;
+                                  k_3 = mapping.fields[0];
+                                  v_2 = head(mapping.fields[1].fields[0]).fields[0];
+                                } else {
+                                  matchResult_3 = 1;
+                                }
+                              } else {
+                                matchResult_3 = 1;
+                              }
+                            } else {
+                              matchResult_3 = 1;
+                            }
+                          } else {
+                            matchResult_3 = 1;
+                          }
+                        } else {
+                          matchResult_3 = 1;
+                        }
+                      } else {
+                        matchResult_3 = 1;
+                      }
+                      switch (matchResult_3) {
+                        case 0: {
+                          void paths.push(v_2.Value);
+                          break;
+                        }
+                      }
+                    }
+                  } finally {
+                    disposeSafe(enumerator_1);
+                  }
+                }
+              }
+            } finally {
+              disposeSafe(enumerator);
+            }
+            return new CWLParameterReference(key, paths, CWLType_Array(new InputArraySchema(CWLType_File(FileInstance_$ctor()), void 0, void 0, void 0)));
+          } else {
+            return new CWLParameterReference(key, []);
+          }
+        default:
+          return new CWLParameterReference(key, resizearray(string, YAMLElement_Sequence(s)));
+      }
+    }
     default:
       throw new Error(`${yEle}`);
   }
@@ -646,4 +1281,4 @@ function DecodeParameters_decodeYAMLParameterFile(yaml) {
   return DecodeParameters_cwlparameterReferenceArrayDecoder(read(yaml));
 }
 
-export { DecodeParameters_cwlParameterReferenceDecoder, DecodeParameters_cwlparameterReferenceArrayDecoder, DecodeParameters_decodeYAMLParameterFile, Decode_baseCommandDecoder, Decode_classDecoder, Decode_commandLineToolDecoder, Decode_cwlArrayTypeDecoder, Decode_cwlTypeDecoder, Decode_cwlTypeStringMatcher, Decode_decodeCWLProcessingUnit, Decode_decodeCommandLineTool, Decode_decodeStringOrExpression, Decode_decodeWorkflow, Decode_direntDecoder, Decode_dockerRequirementDecoder, Decode_envVarRequirementDecoder, Decode_hintsDecoder, Decode_initialWorkDirRequirementDecoder, Decode_inputArrayDecoder, Decode_inputBindingDecoder, Decode_inputStepDecoder, Decode_inputsDecoder, Decode_outputArrayDecoder, Decode_outputBindingDecoder, Decode_outputBindingGlobDecoder, Decode_outputSourceDecoder, Decode_outputStepsDecoder, Decode_outputsDecoder, Decode_overflowDecoder, Decode_requirementArrayDecoder, Decode_requirementsDecoder, Decode_resourceRequirementDecoder, Decode_schemaDefRequirementDecoder, Decode_softwareRequirementDecoder, Decode_stepArrayDecoder, Decode_stepsDecoder, Decode_stringFieldDecoder, Decode_stringOptionFieldDecoder, Decode_toolTimeLimitRequirementDecoder, Decode_versionDecoder, Decode_workflowDecoder, ResizeArray_map };
+export { DecodeParameters_cwlParameterReferenceDecoder, DecodeParameters_cwlparameterReferenceArrayDecoder, DecodeParameters_decodeYAMLParameterFile, Decode_baseCommandDecoder, Decode_classDecoder, Decode_commandLineToolDecoder, Decode_cwlSimpleTypeFromString, Decode_cwlTypeDecoder, Decode_cwlTypeDecoder$0027, Decode_cwlTypeStringMatcher, Decode_decodeCWLProcessingUnit, Decode_decodeCommandLineTool, Decode_decodeStringOrExpression, Decode_decodeWorkflow, Decode_direntDecoder, Decode_docDecoder, Decode_dockerRequirementDecoder, Decode_envVarRequirementDecoder, Decode_hintsDecoder, Decode_initialWorkDirRequirementDecoder, Decode_inputArrayDecoder, Decode_inputArraySchemaDecoder, Decode_inputBindingDecoder, Decode_inputEnumSchemaDecoder, Decode_inputRecordFieldDecoder, Decode_inputRecordSchemaDecoder, Decode_inputStepDecoder, Decode_inputsDecoder, Decode_labelDecoder, Decode_outputArrayDecoder, Decode_outputBindingDecoder, Decode_outputBindingGlobDecoder, Decode_outputSourceDecoder, Decode_outputStepsDecoder, Decode_outputsDecoder, Decode_overflowDecoder, Decode_requirementArrayDecoder, Decode_requirementsDecoder, Decode_resourceRequirementDecoder, Decode_schemaDefRequirementDecoder, Decode_softwareRequirementDecoder, Decode_sourceArrayFieldDecoder, Decode_stepArrayDecoder, Decode_stepsDecoder, Decode_stringFieldDecoder, Decode_stringOptionFieldDecoder, Decode_toolTimeLimitRequirementDecoder, Decode_versionDecoder, Decode_workflowDecoder, ResizeArray_map, inputArraySchemaDecoder$004090, inputArraySchemaDecoder$004090$002D1, inputEnumSchemaDecoder$0040154, inputEnumSchemaDecoder$0040154$002D1, inputRecordFieldDecoder$0040104, inputRecordFieldDecoder$0040104$002D1, inputRecordSchemaDecoder$0040121, inputRecordSchemaDecoder$0040121$002D1 };