Squashed 'cwltool/schemas/' changes from 3e1b02c..0c275b4

0c275b4 clarify that outputBinding must not be set
c30b79f finish restoring allowable types for parameters
06c9ba7 Merge pull request #230 from common-workflow-language/stderr-out-types
cbd7bc2 only allow use of stderr/stdout shortcuts as types for the Outputs. Better place the docs
0ba703d jsonldPredicate did it!
a5a7516 nope, use an enum instead
24a611d use long ids?
52f6411 extend doc to stderr psuedotype
9d0fbe0 initial stdout & stderr shortcut support
392be2f fixing site build?
57a5bc8 Fix last test using "args"
3cc79d2 Port draft-3 changes to command line generation tests to draft-4.
f2a18c3 Add missing args.py used by draft-3 tests.
ac17f5d Port draft-2 changes to command line generation tests to draft-3.
ddf417b Command line generation tests now work by executing a small script that copies the command line to the output.  Allows cwl-runner implementations to drop the --conformance-test code path.
c4cecad Merge pull request #228 from common-workflow-language/scoped-ref-and-typedsl
d1d53b3 Merge pull request #227 from common-workflow-language/stderr
0b987d3 add test
71e9b3d add stderr object
347c28e Merge pull request #212 from common-workflow-language/cwl-runner-interface
28f64f0 clarify description
d791500 add output stanza, fix syntax
ee0bea3 add descriptions
04dfbf0 toolfile is optional
b1e740e bind and order the tool and jobfiles
81bd8de description
c7a2bf1 move to a better location
979453a initial description of cwl-runner interface

git-subtree-dir: cwltool/schemas
git-subtree-split: 0c275b4

Author: mr-c

draft-2/conformance_test_draft-2.yaml

@@ -1,63 +1,52 @@
-- args: [bwa, mem, -t, '4', -I, '1,2,3,4', -m, '3', draft-2/rabix/tests/test-files/chr20.fa,
-    draft-2/rabix/tests/test-files/example_human_Illumina.pe_1.fastq, draft-2/rabix/tests/test-files/example_human_Illumina.pe_2.fastq]
+- args:
   job: draft-2/bwa-mem-job.json
-  stdout: output.sam
   tool: draft-2/bwa-mem-tool.cwl
+  output:
+    args: [bwa, mem, -t, '4', -I, '1,2,3,4', -m, '3',
+      chr20.fa,
+      example_human_Illumina.pe_1.fastq,
+      example_human_Illumina.pe_2.fastq]
   doc: General test of command line generation
 
-- args: [bwa, mem, draft-2/rabix/tests/test-files/chr20.fa,
-    "-XXX",
-    "-YYY", draft-2/rabix/tests/test-files/example_human_Illumina.pe_1.fastq,
-    "-YYY", draft-2/rabix/tests/test-files/example_human_Illumina.pe_2.fastq]
+- output:
+    args: [bwa, mem, chr20.fa,
+      "-XXX",
+      "-YYY", example_human_Illumina.pe_1.fastq,
+      "-YYY", example_human_Illumina.pe_2.fastq]
   job: draft-2/bwa-mem-job.json
   tool: draft-2/binding-test.cwl
   doc: Test nested prefixes with arrays
 
-- args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
+- output:
+    args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
     '20', stage2, map1, --max-seq-length, '20', --min-seq-length, '10', --seed-length,
     '16', map2, --max-seed-hits, '-1', --max-seq-length, '20', --min-seq-length, '10']
   job: draft-2/tmap-job.json
-  stdin: draft-2/reads.fastq
-  stdout: output.sam
   tool: draft-2/tmap-tool.cwl
-  doc: Test nested command line bindings and stdin/stdout redirection
+  doc: Test nested command line bindings
 
-- args: [cat, draft-2/hello.txt]
+- output:
+    args: [cat, hello.txt]
   job: draft-2/cat-job.json
-  tool: draft-2/cat1-tool.cwl
+  tool: draft-2/cat1-testcli.cwl
   doc: Test command line with optional input (missing)
 
-- args: [cat, -n, draft-2/hello.txt]
+- output:
+    args: [cat, -n, hello.txt]
   job: draft-2/cat-n-job.json
-  tool: draft-2/cat1-tool.cwl
+  tool: draft-2/cat1-testcli.cwl
   doc: Test command line with optional input (provided)
 
-- args: [cat]
-  job: draft-2/cat-job.json
-  stdin: draft-2/hello.txt
-  tool: draft-2/cat2-tool.cwl
-  doc: Test command line with stdin redirection
-
-- args: [cat, draft-2/hello.txt]
-  job: draft-2/cat-job.json
-  stdout: output.txt
-  tool: draft-2/cat3-tool.cwl
-  doc: Test command line with stdout redirection
-
-- args: [cat]
-  job: draft-2/cat-job.json
-  stdin: draft-2/hello.txt
-  stdout: output.txt
-  tool: draft-2/cat4-tool.cwl
-  doc: Test command line with stdin and stdout redirection
-
-- args: [cat, foo.txt]
-  createfiles: {foo.txt: 'The file is draft-2/hello.txt
-
-      '}
+- output:
+    "foo": {
+        "checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
+        "class": "File",
+        "path": "foo.txt",
+        "size": 22
+    }
   job: draft-2/cat-job.json
   tool: draft-2/template-tool.cwl
-  doc: Test CreateFileRequirement ExpressionEngineRequirement.engineConfig features
+  doc: Test CreateFileRequirement ExpressionEngineRequirement.engineConfig feature
 
 - job: draft-2/cat-job.json
   output:

draft-2/draft-2/args.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+import sys
+import json
+import os
+args = [os.path.basename(a) for a in sys.argv[1:]]
+with open("cwl.output.json", "w") as f:
+    json.dump({"args": args}, f)

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

@@ -14,6 +14,15 @@ inputs:
       inputBinding: { prefix: "-YYY" }
     inputBinding: { position: 3, prefix: "-XXX" }
 
+  - id: "#args.py"
+    type: File
+    default:
+      class: File
+      path: args.py
+    inputBinding:
+      position: -1
+
 outputs: []
 
-baseCommand: ["bwa", "mem"]
+baseCommand: python
+arguments: ["bwa", "mem"]

draft-2/draft-2/bwa-mem-job.json

@@ -1,18 +1,18 @@
 {
     "reference": {
         "class": "File",
-        "path": "rabix/tests/test-files/chr20.fa",
+        "path": "chr20.fa",
         "size": 123,
         "checksum": "sha1$hash"
     },
     "reads": [
         {
             "class": "File",
-            "path": "rabix/tests/test-files/example_human_Illumina.pe_1.fastq"
+            "path": "example_human_Illumina.pe_1.fastq"
         },
         {
             "class": "File",
-            "path": "rabix/tests/test-files/example_human_Illumina.pe_2.fastq"
+            "path": "example_human_Illumina.pe_2.fastq"
         }
     ],
     "min_std_max_min": [

draft-2/draft-2/bwa-mem-tool.cwl

@@ -4,11 +4,6 @@ class: CommandLineTool
 requirements:
   - import: node-engine.cwl
 
-hints:
-  - class: DockerRequirement
-    dockerPull: images.sbgenomics.com/rabix/bwa
-    dockerImageId: 9d3b9b0359cf
-
 inputs:
   - id: "#reference"
     type: File
@@ -31,14 +26,28 @@ inputs:
       prefix: "-I"
       itemSeparator: ","
 
+  - id: "#args.py"
+    type: File
+    default:
+      class: File
+      path: args.py
+    inputBinding:
+      position: -1
+
 outputs:
   - id: "#sam"
-    type: "File"
+    type: ["null", "File"]
     outputBinding: { "glob": "output.sam" }
+  - id: "#args"
+    type:
+      type: array
+      items: string
 
-baseCommand: ["bwa", "mem"]
+baseCommand: python
 
 arguments:
+  - "bwa"
+  - "mem"
   - valueFrom:
       engine: "node-engine.cwl"
       script: "$job.allocatedResources.cpu"

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

@@ -0,0 +1,34 @@
+#!/usr/bin/env cwl-runner
+{
+    "class": "CommandLineTool",
+    "description": "Print the contents of a file to stdout using 'cat' running in a docker container.",
+    "inputs": [
+        {
+            "id": "#file1",
+            "type": "File",
+            "inputBinding": {"position": 1}
+        },
+        {
+            "id": "#numbering",
+            "type": ["null", "boolean"],
+            "inputBinding": {
+                "position": 0,
+                "prefix": "-n"
+            }
+        },
+        {
+        id: "#args.py",
+        type: File,
+        default: {
+          class: File,
+          path: args.py
+        },
+        inputBinding: {
+          position: -1
+        }
+      }
+    ],
+    "outputs": [],
+    "baseCommand": "python",
+    "arguments": ["cat"]
+}

draft-2/draft-2/cat2-tool.cwl

@@ -17,9 +17,14 @@ requirements:
       - filename: foo.txt
         fileContent:
           engine: "#js"
-          script: 't("The file is <%= $job.file1.path %>\n")'
+          script: >
+            t("The file is <%= $job.file1.path.split('/').slice(-1)[0] %>\n")
 inputs:
   - id: "#file1"
     type: File
-outputs: []
+outputs:
+  - id: "#foo"
+    type: File
+    outputBinding:
+      glob: foo.txt
 baseCommand: ["cat", "foo.txt"]

draft-2/draft-2/chr20.fa

@@ -16,15 +16,26 @@
                 "type": "array",
                 "items": "Stage"
             }
+        },
+        {
+        id: "#args.py",
+        type: File,
+        default: {
+          class: File,
+          path: args.py
+        },
+        inputBinding: {
+          position: -1
         }
+      }
     ],
     "outputs": [
         {
             "id": "#sam",
             "outputBinding": {
                 "glob": "output.sam"
             },
-            "type": "File"
+            "type": ["null", "File"]
         }
     ],
     "requirements": [
@@ -233,10 +244,6 @@
             ]
         }
     ]}],
-    "baseCommand": ["tmap", "mapall"],
-    "stdin": {
-      "engine": "cwl:JsonPointer",
-      "script": "job/reads/path"
-      },
-    "stdout": "output.sam"
+    "baseCommand": "python",
+    "arguments": ["tmap", "mapall"]
 }

draft-2/draft-2/example_human_Illumina.pe_1.fastq

@@ -1,63 +1,51 @@
-- args: [bwa, mem, -t, '4', -I, '1,2,3,4', -m, '3', draft-3/rabix/tests/test-files/chr20.fa,
-    draft-3/rabix/tests/test-files/example_human_Illumina.pe_1.fastq, draft-3/rabix/tests/test-files/example_human_Illumina.pe_2.fastq]
-  job: draft-3/bwa-mem-job.json
-  stdout: output.sam
+- job: draft-3/bwa-mem-job.json
   tool: draft-3/bwa-mem-tool.cwl
+  output:
+    args: [bwa, mem, -t, '4', -I, '1,2,3,4', -m, '3',
+      chr20.fa,
+      example_human_Illumina.pe_1.fastq,
+      example_human_Illumina.pe_2.fastq]
   doc: General test of command line generation
 
-- args: [bwa, mem, draft-3/rabix/tests/test-files/chr20.fa,
-    "-XXX",
-    "-YYY", draft-3/rabix/tests/test-files/example_human_Illumina.pe_1.fastq,
-    "-YYY", draft-3/rabix/tests/test-files/example_human_Illumina.pe_2.fastq]
+- output:
+    args: [bwa, mem, chr20.fa,
+      "-XXX",
+      "-YYY", example_human_Illumina.pe_1.fastq,
+      "-YYY", example_human_Illumina.pe_2.fastq]
   job: draft-3/bwa-mem-job.json
   tool: draft-3/binding-test.cwl
   doc: Test nested prefixes with arrays
 
-- args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
+- output:
+    args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
     '20', stage2, map1, --max-seq-length, '20', --min-seq-length, '10', --seed-length,
     '16', map2, --max-seed-hits, '-1', --max-seq-length, '20', --min-seq-length, '10']
   job: draft-3/tmap-job.json
-  stdin: draft-3/reads.fastq
-  stdout: output.sam
   tool: draft-3/tmap-tool.cwl
-  doc: Test nested command line bindings and stdin/stdout redirection
+  doc: Test nested command line bindings
 
-- args: [cat, draft-3/hello.txt]
+- output:
+    args: [cat, hello.txt]
   job: draft-3/cat-job.json
-  tool: draft-3/cat1-tool.cwl
+  tool: draft-3/cat1-testcli.cwl
   doc: Test command line with optional input (missing)
 
-- args: [cat, -n, draft-3/hello.txt]
+- output:
+    args: [cat, -n, hello.txt]
   job: draft-3/cat-n-job.json
-  tool: draft-3/cat1-tool.cwl
+  tool: draft-3/cat1-testcli.cwl
   doc: Test command line with optional input (provided)
 
-- args: [cat]
-  job: draft-3/cat-job.json
-  stdin: draft-3/hello.txt
-  tool: draft-3/cat2-tool.cwl
-  doc: Test command line with stdin redirection
-
-- args: [cat, draft-3/hello.txt]
-  job: draft-3/cat-job.json
-  stdout: output.txt
-  tool: draft-3/cat3-tool.cwl
-  doc: Test command line with stdout redirection
-
-- args: [cat]
-  job: draft-3/cat-job.json
-  stdin: draft-3/hello.txt
-  stdout: output.txt
-  tool: draft-3/cat4-tool.cwl
-  doc: Test command line with stdin and stdout redirection
-
-- args: [cat, foo.txt]
-  createfiles: {foo.txt: 'The file is draft-3/hello.txt
-
-      '}
+- output:
+    "foo": {
+        "checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
+        "class": "File",
+        "path": "foo.txt",
+        "size": 22
+    }
   job: draft-3/cat-job.json
   tool: draft-3/template-tool.cwl
-  doc: Test CreateFileRequirement ExpressionEngineRequirement.engineConfig features
+  doc: Test CreateFileRequirement ExpressionEngineRequirement.engineConfig feature
 
 - job: draft-3/cat-job.json
   output:
@@ -504,7 +492,7 @@
   doc: |
     Test parameter evaluation, with support for JS expressions
 
-- args: [cat, draft-3/hello.txt]
+- output: {}
   job: draft-3/cat-job.json
   tool: draft-3/metadata.cwl
   doc: Test metadata