Merge commit '31dbd19007690724cfe3e88a64201afca724c681' into inline-expressions

Author: Peter Amstutz

cwltool/schemas/draft-2/draft-2/add-lines-wf.cwl

@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: "cwl:draft-3.dev2"
+
+inputs:
+  - id: reference
+    type: File
+    inputBinding: { position: 2 }
+
+  - id: reads
+    type:
+      type: array
+      items: File
+      inputBinding: { prefix: "-YYY" }
+    inputBinding: { position: 3, prefix: "-XXX" }
+
+outputs: []
+
+baseCommand: [bwa, mem]

cwltool/schemas/draft-3/draft-3/add-lines-wf.cwl

@@ -0,0 +1,29 @@
+{
+    "reference": {
+        "class": "File",
+        "path": "rabix/tests/test-files/chr20.fa",
+        "size": 123,
+        "checksum": "sha1$hash"
+    },
+    "reads": [
+        {
+            "class": "File",
+            "path": "rabix/tests/test-files/example_human_Illumina.pe_1.fastq"
+        },
+        {
+            "class": "File",
+            "path": "rabix/tests/test-files/example_human_Illumina.pe_2.fastq"
+        }
+    ],
+    "min_std_max_min": [
+        1,
+        2,
+        3,
+        4
+    ],
+    "minimum_seed_length": 3,
+    "allocatedResources": {
+        "cpu": 4,
+        "mem": 5000
+    }
+}

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

@@ -1,50 +1,46 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: "cwl:draft-3.dev1"
+cwlVersion: "cwl:draft-3.dev2"
 
 class: CommandLineTool
-requirements:
-  - "@import": node-engine.cwl
 
 hints:
   - class: DockerRequirement
     dockerPull: images.sbgenomics.com/rabix/bwa
     dockerImageId: 9d3b9b0359cf
 
 inputs:
-  - id: "#reference"
+  - id: reference
     type: File
     inputBinding: { position: 2 }
 
-  - id: "#reads"
+  - id: reads
     type:
       type: array
       items: File
     inputBinding: { position: 3 }
 
-  - id: "#minimum_seed_length"
+  - id: minimum_seed_length
     type: int
-    inputBinding: { position: 1, prefix: "-m" }
+    inputBinding: { position: 1, prefix: -m }
 
-  - id: "#min_std_max_min"
+  - id: min_std_max_min
     type: { type: array, items: int }
     inputBinding:
       position: 1
-      prefix: "-I"
+      prefix: -I
       itemSeparator: ","
 
 outputs:
-  - id: "#sam"
-    type: "File"
-    outputBinding: { "glob": "output.sam" }
+  - id: sam
+    type: File
+    outputBinding: { glob: output.sam }
 
-baseCommand: ["bwa", "mem"]
+baseCommand: [bwa, mem]
 
 arguments:
-  - valueFrom:
-      engine: "node-engine.cwl"
-      script: "$job.allocatedResources.cpu"
+  - valueFrom: $(inputs.allocatedResources.cores)
     position: 1
-    prefix: "-t"
+    prefix: -t
 
-stdout: "output.sam"
+stdout: output.sam

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

@@ -0,0 +1,6 @@
+{
+    "file1": {
+        "class": "File",
+        "path": "hello.txt"
+    }
+}

cwltool/schemas/draft-3/draft-3/bwa-mem-job.json

@@ -0,0 +1,7 @@
+{
+    "file1": {
+        "class": "File",
+        "path": "hello.txt"
+    },
+    "numbering": true
+}

cwltool/schemas/draft-3/draft-3/bwa-mem-job.json

@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: "cwl:draft-3.dev2"
+class: CommandLineTool
+description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+hints:
+  - class: DockerRequirement
+    dockerPull: debian:wheezy
+inputs: [
+  - id: file1
+    type: File
+    inputBinding: {position: 1}
+  - id: numbering
+    type: ["null", boolean]
+    inputBinding:
+      position: 0
+      prefix: -n
+outputs: []
+baseCommand: cat

cwltool/schemas/draft-3/draft-3/bwa-mem-tool.cwl

@@ -0,0 +1,13 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: "cwl:draft-3.dev2"
+description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+hints:
+  - class: DockerRequirement
+    dockerPull: debian:wheezy
+inputs:
+  - id: file1
+    type: File
+outputs: []
+baseCommand: cat
+stdin: $(inputs.file1.path)

cwltool/schemas/draft-3/draft-3/cat-job.json

@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: "cwl:draft-3.dev2"
+description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+hints:
+  - class: DockerRequirement
+    dockerPull: debian:wheezy
+inputs:
+  - id: file1
+    type: File
+    label: Input File
+    description: "The file that will be copied using 'cat'"
+    inputBinding: {position: 1}
+outputs:
+  - id: output_file
+    type: File
+    outputBinding: {glob: output.txt}
+baseCommand: cat
+stdout: output.txt

cwltool/schemas/draft-3/draft-3/cat-job.json

@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: "cwl:draft-3.dev2"
+description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+hints:
+  - class: DockerRequirement
+    dockerPull: debian:wheezy
+inputs:
+  - id: file1
+    type: File
+outputs:
+  - id: output_txt
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: cat
+stdout: output.txt
+stdin: $(inputs.file1.path)

cwltool/schemas/draft-3/draft-3/cat-n-job.json

@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: "cwl:draft-3.dev2"
+class: CommandLineTool
+description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+hints:
+  - class: DockerRequirement
+    dockerPull: "debian:wheezy"
+  - class: BlibberBlubberFakeRequirement
+    fakeField: fraggleFroogle
+inputs:
+  - id: file1
+    type: File
+    label: "Input File"
+    description: "The file that will be copied using 'cat'"
+    inputBinding: {position: 1}
+outputs:
+  - id: output_file
+    type: File
+    outputBinding: {glob: output.txt}
+baseCommand: cat
+stdout: output.txt

cwltool/schemas/draft-3/draft-3/cat-n-job.json

@@ -1,26 +1,26 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: "cwl:draft-3.dev1"
+cwlVersion: "cwl:draft-3.dev2"
 
 inputs:
-  - { id: "#file1", type: File }
+  - { id: file1, type: File }
 
 outputs:
-  - id: "#count_output"
+  - id: count_output
     type: int
-    source: "#step2.output"
+    source: "#step2/output"
 
 steps:
-  - id: "#step1"
+  - id: step1
     run: {"@import": wc-tool.cwl}
     inputs:
-      - {id: "#step1.file1", source: "#file1"}
+      - {id: file1, source: "#file1"}
     outputs:
-      - {id: "#step1.output"}
+      - {id: output}
 
-  - id: "#step2"
+  - id: step2
     run: {"@import": parseInt-tool.cwl}
     inputs:
-      - {id: "#step2.file1", source: "#step1.output"}
+      - {id: file1, source: "#step1/output"}
     outputs:
-      - {id: "#step2.output"}
+      - {id: output}

cwltool/schemas/draft-3/draft-3/cat1-tool.cwl

@@ -1,16 +1,13 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: "cwl:draft-3.dev1"
+cwlVersion: "cwl:draft-3.dev2"
 
 inputs:
     - { id: file1, type: File }
 
 outputs:
     - { id: count_output, type: int, source: "#step2/parseInt_output"}
 
-requirements:
-  - "@import": node-engine.cwl
-
 steps:
   - id: step1
     inputs:
@@ -25,21 +22,13 @@ steps:
       outputs:
         - { id: wc_output, type: File, outputBinding: { glob: output.txt } }
       stdout: output.txt
-      baseCommand: ["wc"]
+      baseCommand: wc
 
   - id: step2
     inputs:
-      - { "id": parseInt_file1, source: "#step1/wc_output" }
+      - { id: parseInt_file1, source: "#step1/wc_output" }
     outputs:
-      - { "id": parseInt_output }
+      - { id: parseInt_output }
     run:
-      id: parseInt
       class: ExpressionTool
-      inputs:
-        - { id: parseInt_file1, type: File, inputBinding: { loadContents: true } }
-      outputs:
-        - { id: parseInt_output, type: int }
-      expression:
-        engine: node-engine.cwl
-        script: >
-          {return {'parseInt_output': parseInt($job.parseInt_file1.contents)};}
+      expression: ${return {'parseInt_output': parseInt($job.parseInt_file1.contents)};}

cwltool/schemas/draft-3/draft-3/cat1-tool.cwl

@@ -0,0 +1,12 @@
+{
+    "file1": [
+        {
+            "class": "File",
+            "path": "whale.txt"
+        },
+        {
+            "class": "File",
+            "path": "hello.txt"
+        }
+    ]
+}