Squashed 'cwltool/schemas/' changes from c4cfafb..f027dbb

f027dbb Permit idmaps for hints, envDef
899d135 Update conformance tests to use draft-4 syntax improvements.
2c14f2f Update conformance tests with draft-4 version number.
e562b21 Merge branch 'draft-4' of github.com:common-workflow-language/common-workflow-language into draft-4
9b737de Changed name for initial working directory

git-subtree-dir: cwltool/schemas
git-subtree-split: f027dbb

Author: Peter Amstutz

draft-4/CommandLineTool.yml

@@ -244,7 +244,7 @@ $graph:
         the File objects must include up to the first 64 KiB of file contents
         in the `contents` field.
 
-- name: InitialWorkingDirectory
+- name: initialWorkDir
   type: record
   doc: |
     Setup a working directory based on a number of input files (and/or directories)
@@ -562,6 +562,9 @@ $graph:
         type: "array"
         items: "#EnvironmentDef"
       doc: The list of environment variables.
+      jsonldPredicate:
+        mapSubject: envName
+        mapPredicate: envValue
 
 
 - type: record

draft-4/Process.yml

@@ -520,9 +520,6 @@ $graph:
         - "null"
         - type: array
           items: Any
-      jsonldPredicate:
-        _id: "cwl:hints"
-        mapSubject: class
       doc: |
         Declares hints applying to either the runtime environment or the
         workflow engine that may be helpful in executing this process.  It is
@@ -531,6 +528,7 @@ $graph:
       jsonldPredicate:
         _id: cwl:hints
         noLinkCheck: true
+        mapSubject: class
     - name: label
       type:
         - "null"

draft-4/Workflow.yml

@@ -324,15 +324,13 @@ $graph:
           items: "Any"
       jsonldPredicate:
         _id: "cwl:hints"
+        noLinkCheck: true
         mapSubject: class
       doc: |
         Declares hints applying to either the runtime environment or the
         workflow engine that may be helpful in executing this workflow step.  It is
         not an error if an implementation cannot satisfy all hints, however
         the implementation may report a warning.
-      jsonldPredicate:
-        _id: cwl:hints
-        noLinkCheck: true
     - name: label
       type:
         - "null"
@@ -441,7 +439,8 @@ $graph:
       type:
         - type: array
           items: "#WorkflowStep"
-
+      jsonldPredicate:
+          mapSubject: id
 
 
 - type: record

draft-4/draft-4/binding-test.cwl

@@ -1,14 +1,14 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 
 inputs:
-  - id: reference
+  reference:
     type: File
     inputBinding: { position: 2 }
 
-  - id: reads
+  reads:
     type:
       type: array
       items: File

draft-4/draft-4/bwa-mem-tool.cwl

@@ -1,41 +1,41 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 
 class: CommandLineTool
 
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: images.sbgenomics.com/rabix/bwa
     dockerImageId: 9d3b9b0359cf
 
-  - class: ResourceRequirement
+  ResourceRequirement:
     coresMin: 4
 
 inputs:
-  - id: reference
+  reference:
     type: File
     inputBinding: { position: 2 }
 
-  - id: reads
+  reads:
     type:
       type: array
       items: File
     inputBinding: { position: 3 }
 
-  - id: minimum_seed_length
+  minimum_seed_length:
     type: int
     inputBinding: { position: 1, prefix: -m }
 
-  - id: min_std_max_min
+  min_std_max_min:
     type: { type: array, items: int }
     inputBinding:
       position: 1
       prefix: -I
       itemSeparator: ","
 
 outputs:
-  - id: sam
+  sam:
     type: File
     outputBinding: { glob: output.sam }
 

draft-4/draft-4/cat1-tool.cwl

@@ -1,15 +1,15 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
     inputBinding: {position: 1}
-  - id: numbering
+  numbering:
     type: ["null", boolean]
     inputBinding:
       position: 0

draft-4/draft-4/cat2-tool.cwl

@@ -1,12 +1,12 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
 outputs: []
 baseCommand: cat

draft-4/draft-4/cat3-tool.cwl

@@ -1,18 +1,18 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
     label: Input File
     description: "The file that will be copied using 'cat'"
     inputBinding: {position: 1}
 outputs:
-  - id: output_file
+  output_file:
     type: File
     outputBinding: {glob: output.txt}
 baseCommand: cat

draft-4/draft-4/cat4-tool.cwl

@@ -1,15 +1,15 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
 outputs:
-  - id: output_txt
+  output_txt:
     type: File
     outputBinding:
       glob: output.txt

draft-4/draft-4/cat5-tool.cwl

@@ -1,20 +1,20 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: "debian:wheezy"
-  - class: BlibberBlubberFakeRequirement
+  BlibberBlubberFakeRequirement:
     fakeField: fraggleFroogle
 inputs:
-  - id: file1
+  file1:
     type: File
     label: "Input File"
     description: "The file that will be copied using 'cat'"
     inputBinding: {position: 1}
 outputs:
-  - id: output_file
+  output_file:
     type: File
     outputBinding: {glob: output.txt}
 baseCommand: cat

draft-4/draft-4/conflict-wf.cwl

@@ -1,35 +1,35 @@
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 $graph:
-- class: CommandLineTool
-  id: echo
+- id: echo
+  class: CommandLineTool
   inputs:
-    - id: text
+    text:
       type: string
       inputBinding: {}
 
   outputs:
-    - id: fileout
+    fileout:
       type: File
       outputBinding:
         glob: out.txt
 
   baseCommand: echo
   stdout: out.txt
 
-- class: CommandLineTool
-  id: cat
+- id: cat
+  class: CommandLineTool
   inputs:
-    - id: file1
+    file1:
       type: File
       inputBinding:
         position: 1
-    - id: file2
+    file2:
       type: File
       inputBinding:
         position: 2
 
   outputs:
-    - id: fileout
+    fileout:
       type: File
       outputBinding:
         glob: out.txt
@@ -41,40 +41,35 @@ $graph:
   id: collision
 
   inputs:
-    - id: input_1
+    input_1:
       type: string
 
-    - id: input_2
+    input_2:
       type: string
 
   outputs:
-    - id: fileout
+    fileout:
       type: File
       source: "#collision/cat_step/fileout"
 
   steps:
-    - id: echo_1
+    echo_1:
       run: "#echo"
-      inputs:
-        - id: text
-          source: "#collision/input_1"
-      outputs:
-        - id: fileout
+      in:
+        text: "#collision/input_1"
+      out: [fileout]
 
-    - id: echo_2
+    echo_2:
       run: "#echo"
-      inputs:
-        - id: text
-          source: "#collision/input_2"
-      outputs:
-        - id: fileout
+      in:
+        text: "#collision/input_2"
+      out: [fileout]
 
-    - id: cat_step
+    cat_step:
       run: "#cat"
-      inputs:
-        - id: file1
+      in:
+        file1:
           source: "#collision/echo_1/fileout"
-        - id: file2
+        file2:
           source: "#collision/echo_2/fileout"
-      outputs:
-        - id: fileout
+      out: [fileout]

draft-4/draft-4/count-lines1-wf.cwl

@@ -1,26 +1,25 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev1
 
 inputs:
-  - { id: file1, type: File }
+  file1:
+    type: File
 
 outputs:
-  - id: count_output
+  count_output:
     type: int
     source: "#step2/output"
 
 steps:
-  - id: step1
+  step1:
     run: wc-tool.cwl
-    inputs:
-      - {id: file1, source: "#file1"}
-    outputs:
-      - {id: output}
+    in:
+      file1: "#file1"
+    out: [output]
 
-  - id: step2
+  step2:
     run: parseInt-tool.cwl
-    inputs:
-      - {id: file1, source: "#step1/output"}
-    outputs:
-      - {id: output}
+    in:
+      file1: "#step1/output"
+    out: [output]