Merge pull request #303 from common-workflow-language/include-stdin-in-docs

put stdin shortcut in correct place

Author: mr-c

v1.1.0-dev1/CommandLineTool.yml

@@ -367,14 +367,32 @@ $graph:
   extends: InputParameter
   doc: An input parameter for a CommandLineTool.
   specialize:
-    - specializeFrom: InputRecordSchema
-      specializeTo: CommandInputRecordSchema
-    - specializeFrom: InputEnumSchema
-      specializeTo: CommandInputEnumSchema
-    - specializeFrom: InputArraySchema
-      specializeTo: CommandInputArraySchema
     - specializeFrom: InputBinding
       specializeTo: CommandLineBinding
+  fields:
+    - name: type
+      type:
+        - "null"
+        - CWLType
+        - stdin
+        - CommandInputRecordSchema
+        - CommandInputEnumSchema
+        - CommandInputArraySchema
+        - string
+        - type: array
+          items:
+            - CWLType
+            - CommandInputRecordSchema
+            - CommandInputEnumSchema
+            - CommandInputArraySchema
+            - string
+      jsonldPredicate:
+        "_id": "sld:type"
+        "_type": "@vocab"
+        refScope: 2
+        typeDSL: True
+      doc: |
+        Specify valid types of data that may be assigned to this parameter.
 
 - type: record
   name: CommandOutputParameter

v1.1.0-dev1/Process.yml

@@ -568,6 +568,10 @@ $graph:
         The default value for this parameter if not provided in the input
         object.
 
+- name: RegularInputParameter
+  type: record
+  extends: InputParameter
+  fields:
     - name: type
       type:
         - "null"
@@ -591,6 +595,7 @@ $graph:
       doc: |
         Specify valid types of data that may be assigned to this parameter.
 
+
 - name: OutputParameter
   type: record
   extends: Parameter

v1.1.0-dev1/Workflow.yml

@@ -87,17 +87,17 @@ $graph:
     - name: type
       type:
         - "null"
-        - "#CWLType"
-        - "#OutputRecordSchema"
-        - "#OutputEnumSchema"
-        - "#OutputArraySchema"
+        - CWLType
+        - OutputRecordSchema
+        - OutputEnumSchema
+        - OutputArraySchema
         - string
         - type: array
           items:
-            - "#CWLType"
-            - "#OutputRecordSchema"
-            - "#OutputEnumSchema"
-            - "#OutputArraySchema"
+            - CWLType
+            - OutputRecordSchema
+            - OutputEnumSchema
+            - OutputArraySchema
             - string
       jsonldPredicate:
         "_id": "sld:type"
@@ -111,13 +111,15 @@ $graph:
   name: ExpressionTool
   extends: Process
   specialize:
-    - specializeFrom: "#OutputParameter"
-      specializeTo: "#ExpressionToolOutputParameter"
+    - specializeFrom: InputParameter
+      specializeTo: RegularInputParameter
+    - specializeFrom: OutputParameter
+      specializeTo: ExpressionToolOutputParameter
   documentRoot: true
   doc: |
     Execute an expression as a Workflow step.
   fields:
-    - name: "class"
+    - name: class
       jsonldPredicate:
         "_id": "@type"
         "_type": "@vocab"
@@ -158,25 +160,25 @@ $graph:
         - string?
         - string[]?
     - name: linkMerge
-      type: ["null", "#LinkMergeMethod"]
+      type: ["null", LinkMergeMethod]
       jsonldPredicate: "cwl:linkMerge"
       doc: |
         The method to use to merge multiple sources into a single array.
         If not specified, the default method is "merge_nested".
     - name: type
       type:
         - "null"
-        - "#CWLType"
-        - "#OutputRecordSchema"
-        - "#OutputEnumSchema"
-        - "#OutputArraySchema"
+        - CWLType
+        - OutputRecordSchema
+        - OutputEnumSchema
+        - OutputArraySchema
         - string
         - type: array
           items:
-            - "#CWLType"
-            - "#OutputRecordSchema"
-            - "#OutputEnumSchema"
-            - "#OutputArraySchema"
+            - CWLType
+            - OutputRecordSchema
+            - OutputEnumSchema
+            - OutputArraySchema
             - string
       jsonldPredicate:
         "_id": "sld:type"
@@ -268,8 +270,8 @@ $graph:
     - name: valueFrom
       type:
         - "null"
-        - "string"
-        - "#Expression"
+        - string
+        - Expression
       jsonldPredicate: "cwl:valueFrom"
       doc: |
         To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
@@ -462,8 +464,10 @@ $graph:
   extends: "#Process"
   documentRoot: true
   specialize:
-    - specializeFrom: "#OutputParameter"
-      specializeTo: "#WorkflowOutputParameter"
+    - specializeFrom: InputParameter
+      specializeTo: RegularInputParameter
+    - specializeFrom: OutputParameter
+      specializeTo: WorkflowOutputParameter
   doc: |
     A workflow describes a set of **steps** and the **dependencies** between
     those steps.  When a step produces output that will be consumed by a