Merge pull request #334 from StarvingMarvin/master

Explicit 'args' output for three tests in draft-2, draft-3 and v1.0

Author: mr-c

draft-2/draft-2/binding-test.cwl

@@ -22,7 +22,11 @@ inputs:
     inputBinding:
       position: -1
 
-outputs: []
+outputs:
+  - id: "#args"
+    type:
+      type: array
+      items: string
 
 baseCommand: python
 arguments: ["bwa", "mem"]

draft-2/draft-2/cat1-testcli.cwl

@@ -17,18 +17,24 @@
             }
         },
         {
-        id: "#args.py",
-        type: File,
-        default: {
-          class: File,
-          path: args.py
-        },
-        inputBinding: {
-          position: -1
-        }
+            "id": "#args.py",
+            "type": "File",
+            "default": {
+              "class": "File",
+              "path": "args.py"
+            },
+            "inputBinding": {
+              "position": -1
+            }
       }
     ],
-    "outputs": [],
+    "outputs": [{
+      "id": "#args",
+      "type": {
+          "type": "array",
+          "items": "string"
+      }
+    }],
     "baseCommand": "python",
     "arguments": ["cat"]
 }

draft-2/draft-2/tmap-tool.cwl

@@ -18,14 +18,14 @@
             }
         },
         {
-        id: "#args.py",
-        type: File,
-        default: {
-          class: File,
-          path: args.py
+        "id": "#args.py",
+        "type": "File",
+        "default": {
+          "class": "File",
+          "path": "args.py"
         },
-        inputBinding: {
-          position: -1
+        "inputBinding": {
+          "position": -1
         }
       }
     ],
@@ -36,6 +36,13 @@
                 "glob": "output.sam"
             },
             "type": ["null", "File"]
+        },
+        {
+            "id": "#args",
+            "type": {
+                "type": "array",
+                "items": "string"
+            }
         }
     ],
     "requirements": [

draft-3/draft-3/binding-test.cwl

@@ -23,7 +23,11 @@ inputs:
     inputBinding:
       position: -1
 
-outputs: []
+outputs:
+  - id: args
+    type:
+      type: array
+      items: string
 
 baseCommand: python
 arguments: ["bwa", "mem"]

draft-3/draft-3/cat1-testcli.cwl

@@ -18,18 +18,24 @@
             }
         },
         {
-        id: "args.py",
-        type: File,
-        default: {
-          class: File,
-          path: args.py
+        "id": "args.py",
+        "type": "File",
+        "default": {
+          "class": "File",
+          "path": "args.py"
         },
-        inputBinding: {
-          position: -1
+        "inputBinding": {
+          "position": -1
         }
       }
     ],
-    "outputs": [],
+    "outputs": [{
+        "id": "args",
+        "type": {
+            "type": "array",
+            "items": "string"
+        }
+    }],
     "baseCommand": "python",
     "arguments": ["cat"]
 }

draft-3/draft-3/tmap-tool.cwl

@@ -20,15 +20,15 @@
             }
         },
         {
-        id: "#args.py",
-        type: File,
-        default: {
-          class: File,
-          path: args.py
-        },
-        inputBinding: {
-          position: -1
-        }
+            "id": "#args.py",
+            "type": "File",
+            "default": {
+              "class": "File",
+              "path": "args.py"
+            },
+            "inputBinding": {
+              "position": -1
+            }
       }
     ],
     "outputs": [
@@ -38,6 +38,13 @@
                 "glob": "output.sam"
             },
             "type": ["null", "File"]
+        },
+        {
+            "id": "args",
+            "type": {
+                "type": "array",
+                "items": "string"
+            }
         }
     ],
     "requirements": [

v1.0/conformance_test_v1.0.yaml

@@ -77,7 +77,7 @@
   tool: v1.0/cat3-tool-mediumcut.cwl
   doc: Test command execution in Docker with stdout redirection
 
-- job:
+- job: v1.0/empty.json
   tool: v1.0/egrep-stderr.cwl
   doc: Test command line with stderr redirection
   output:
@@ -87,7 +87,7 @@
       size: 84
       location: error.txt
 
-- job:
+- job: v1.0/empty.json
   tool: v1.0/egrep-stderr-shortcut.cwl
   doc: Test command line with stderr redirection, brief syntax
   output:
@@ -103,7 +103,7 @@
       size: 84
       checksum: sha1$cec7b8746a78c42060c96505887449bca0142976
       location: std.err
-  job:
+  job: v1.0/empty.json
   tool: v1.0/egrep-stderr-mediumcut.cwl
   doc: Test command line with stderr redirection, named brief syntax
 

v1.0/v1.0/binding-test.cwl

@@ -23,7 +23,8 @@ inputs:
     inputBinding:
       position: -1
 
-outputs: []
+outputs:
+  args: string[]
 
 baseCommand: python
 arguments: ["bwa", "mem"]

v1.0/v1.0/cat1-testcli.cwl

@@ -29,7 +29,7 @@
         }
       }
     ],
-    "outputs": [],
+    "outputs": [{"id": "args", "type": "string[]"}],
     "baseCommand": "python",
     "arguments": ["cat"]
 }

v1.0/v1.0/tmap-tool.cwl

@@ -38,7 +38,8 @@
                 "glob": "output.sam"
             },
             "type": ["null", "File"]
-        }
+        },
+        {"id": "args", "type": "string[]"}
     ],
     "requirements": [
     {"class": "SchemaDefRequirement",