Squashed 'cwltool/schemas/' changes from 1550753..aa320ec

aa320ec Merge pull request common-workflow-language#342 from common-workflow-language/fix-mystery-package-errors 3c6eaff Update for rename of argparse2cwl to argparse2tool b14404b remove errant jsonldPredicate 7f116da Merge pull request common-workflow-language#339 from common-workflow-language/dockerOutputDirectory 4f65d1f Add test for dockerOutputDirectory option of DockerRequirement. cb1f928 Merge pull request common-workflow-language#335 from common-workflow-language/output-literals d8b6c8f Add tests for file and directory literals in output as produced by expression tool. ee3bb1c Merge pull request common-workflow-language#324 from common-workflow-language/secondaryfiles-array 5e6c2d4 Add NLeSC's Xenon cbe1c8d Merge pull request common-workflow-language#334 from StarvingMarvin/master 8300e43 output ids must start with '#' in draft-2 f87d218 draft-3 test fixes: explicit output for args 8b10319 Fixes for draft-2 tests: adding explicit args output 83ed4b4 Merge remote-tracking branch 'rabix-cwl/master' e0a5e7c Merge pull request common-workflow-language#328 from StarvingMarvin/master d906c4a dir4 test fix 21bdcaf Merge remote-tracking branch 'upstream/master' dee0f4e Disabled checksum check for listing input dir fc4cb0f Added args output and empty.json for null jobs a4950f4 Update tools list 8e1d67c Add Rabix Bunny CI badge 2a5b95e fixing mentions to draft3/4 1356c45 Add test for secondaryFiles with arrays b60125b Single instead of double quotes in doc 179835b Merge pull request common-workflow-language#319 from common-workflow-language/test-cwl-out2 ed40737 Add additional test for cwl.output.json behavior. a217bb6 Merge pull request common-workflow-language#317 from StarvingMarvin/master 8dd69f2 fixing test in v1.0 and v1.1.0-dev1 e831c20 Merge pull request common-workflow-language#314 from common-workflow-language/test-requirements-on-steps 8cad6f1 Add test for requirements/hints on workflow steps. 7679adb Merge pull request common-workflow-language#308 from common-workflow-language/embedded-subworkflow-test 1582677 Tighten up formatting 779c2d4 Add test for embedded subworkflow e22a9c2 Merge pull request common-workflow-language#307 from alaindomissy/patch-3 125cb5f Update UserGuide.yml 99f4f9f Merge pull request common-workflow-language#303 from common-workflow-language/include-stdin-in-docs 5324dbb put stdin shortcut in correct place git-subtree-dir: cwltool/schemas git-subtree-split: aa320ec
qiukunlong · Nov 15, 2016 · 65f95a3 · 65f95a3
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diff --git a/README.md b/README.md
@@ -40,16 +40,18 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 
 ## Implementations
 
-|Software|Description|CWL support|Platform support|Maturity|
+|Software|Description|CWL support|Platform support|Platform Maturity|
 |--------|-----------|-----------|--------|--------|
 |[cwltool](https://github.com/common-workflow-language/cwltool)|Reference implementation of CWL|[![Build Status](https://ci.commonwl.org/job/cwltool-conformance/badge/icon)](http://ci.commonwl.org/job/cwltool-conformance/lastBuild/testReport/)|Linux, OS X, local execution only|Production|
 |[Arvados](https://arvados.org)|Distributed computing platform for data analysis on massive data sets. [Using CWL on Arvados](http://doc.arvados.org/user/cwl/cwl-runner.html)|[![Build Status](https://ci.commonwl.org/job/arvados-conformance/badge/icon)](http://ci.commonwl.org/job/arvados-conformance/lastBuild/testReport/)|AWS, GCP, Azure, Slurm|Production|
 |[Toil](https://github.com/BD2KGenomics/toil)|Toil is a workflow engine entirely written in Python.|[![Build Status](https://ci.commonwl.org/job/toil-conformance/badge/icon)](http://ci.commonwl.org/job/toil-conformance/lastBuild/testReport/)|AWS, GCP, Azure, OpenStack, Grid Engine, Mesos|Production|
+|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|[![Build Status](https://ci.commonwl.org/buildStatus/icon?job=rabix-conformance)](https://ci.commonwl.org/job/rabix-conformance/)|Java|alpha|
 |[Apache Taverna](http://taverna.incubator.apache.org/)|Domain-independent Workflow Management System|[alpha](https://issues.apache.org/jira/browse/TAVERNA-900)|Java|Production|
 |[Galaxy](https://galaxyproject.org/)|Web-based platform for data intensive biomedical research.|[alpha](https://github.com/common-workflow-language/galaxy)|Python|Production|
 |[AWE](https://github.com/MG-RAST/AWE)|Workflow and resource management system for bioinformatics data analysis.|[alpha](https://github.com/wgerlach/AWE)|Go|Production|
 |[Funnel](https://github.com/bmeg/funnel)|Use Google Genomics Pipeline API with CWL|alpha|GCP|alpha|
-|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|alpha|Java|alpha|
+|[xenon-cwl-runner](https://github.com/NLeSC/xenon-cwl-runner)|Run CWL workflows using Xenon|alpha|[any Xenon backend](http://nlesc.github.io/Xenon/): local, ssh, SLURM, Torque, Grid Engine|Production|
+
 
 ## Repositories of CWL Tools and Workflows
 
@@ -64,10 +66,12 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 |--------|-----------|
 |[cwltest](https://github.com/common-workflow-language/cwltest)|CWL testing framework,  automated testing of tools and workflows written with CWL|
 |[cwl-upgrader](https://github.com/common-workflow-language/cwl-upgrader)|Upgrade CWL documents from draft-3 to v1.0|
-|[argparse2cwl](https://github.com/common-workflow-language/gxargparse#argparse2cwl)|Generate CWL CommandLineTool wrapper from Python programs that use argparse.  Also supports [click](http://click.pocoo.org/5/) argument parser.|
+|[argparse2tool](https://github.com/erasche/argparse2tool#cwl-specific-functionality)|Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse.  Also supports the [click](http://click.pocoo.org/5/) argument parser.|
 |[cwl2argparse](https://github.com/common-workflow-language/cwl2argparse)|Generate Python argparse code from CWL CommandLineTool description.|
 |[pypi2cwl](https://github.com/common-workflow-language/pypi2cwl)|Automatically run argparse2cwl on any package in PyPi|
 |[cwlavro](https://github.com/common-workflow-language/cwlavro)|Java classes for loading CWL documents|
+|[acd2cwl](https://github.com/common-workflow-language/acd2cwl)|CWL generator for ACD (EMBOSS) files |
+|[CWLviewer](https://github.com/MarkRobbo/CWLViewer)|A web application to view and share Common Workflow Language workflows|
 
 ## Support, Community and Contributing
 

diff --git a/draft-2/draft-2/binding-test.cwl b/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"]
diff --git a/draft-2/draft-2/cat1-testcli.cwl b/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"]
 }
diff --git a/draft-2/draft-2/tmap-tool.cwl b/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": [

diff --git a/draft-3/draft-3/binding-test.cwl b/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"]
diff --git a/draft-3/draft-3/cat1-testcli.cwl b/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"]
 }
diff --git a/draft-3/draft-3/tmap-tool.cwl b/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": [

diff --git a/v1.0/CommandLineTool.yml b/v1.0/CommandLineTool.yml
@@ -694,7 +694,6 @@ $graph:
     - name: package
       type: string
       doc: "The common name of the software to be configured."
-      jsonldPredicate: "@id"
     - name: version
       type: string[]?
       doc: "The (optional) version of the software to configured."

diff --git a/v1.0/UserGuide.yml b/v1.0/UserGuide.yml
@@ -290,8 +290,8 @@
     - |
       ## Parameter references
 
-      In a previous example, we used extracted a file using the "tar" program.
-      However, that example was very limited becuase it assumed that the file
+      In a previous example, we extracted a file using the "tar" program.
+      However, that example was very limited because it assumed that the file
       we were interested in was called "hello.txt".  In this example, you will
       see how to reference the value of input parameters dynamically from other
       fields.

diff --git a/v1.0/concepts.md b/v1.0/concepts.md
@@ -89,7 +89,7 @@ preprocessing steps described in the
 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html).
 An implementation may formally validate the structure of a CWL document using
 SALAD schemas located at
-https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-4
+https://github.com/common-workflow-language/common-workflow-language/tree/master/v1.0
 
 ## Identifiers
 

diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml
@@ -63,7 +63,7 @@
     output_file:
       class: File
       checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
-      location:
+      location: Any
       size: 13
   doc: Test command execution in Docker with simplified syntax stdout redirection
 
@@ -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
 
@@ -287,6 +287,16 @@
   tool: v1.0/env-wf2.cwl
   doc: Test requirements override hints
 
+- job: v1.0/env-job.json
+  output:
+    out:
+      class: File
+      checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6
+      location: out
+      size: 9
+  tool: v1.0/env-wf3.cwl
+  doc: Test requirements on workflow steps
+
 - job: v1.0/empty.json
   output: {count_output: 16}
   tool: v1.0/count-lines9-wf.cwl
@@ -649,7 +659,23 @@
     }
   }
   tool: v1.0/test-cwl-out.cwl
-  doc: Test support for reading cwl.output.json when running in Docker container
+  doc: |
+    Test support for reading cwl.output.json when running in a Docker container
+    and just 'path' is provided.
+
+- job: v1.0/empty.json
+  output: {
+    "foo": {
+        "location": "foo",
+        "class": "File",
+        "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
+        "size": 4
+    }
+  }
+  tool: v1.0/test-cwl-out2.cwl
+  doc: |
+    Test support for reading cwl.output.json when running in a Docker container
+    and just 'location' is provided.
 
 - job: v1.0/abc.json
   output:
@@ -763,10 +789,10 @@
 - job: v1.0/dir4-job.yml
   output: {
     "outlist": {
-        "checksum": "sha1$2ab6f189e84753c05a23413fbf6b6fbf4c53489f",
-        "size": 90,
-        "location": "output.txt",
-        "class": "File"
+      "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592",
+      "size": 20,
+      "location": "output.txt",
+      "class": "File"
     }
   }
   tool: v1.0/dir4.cwl
@@ -883,3 +909,65 @@
       "size": 12010
   tool: v1.0/initialworkdirrequirement-docker-out.cwl
   doc: Test output of InitialWorkDir
+
+- job: v1.0/wc-job.json
+  output: {count_output: 16}
+  tool: v1.0/count-lines10-wf.cwl
+  doc: Test embedded subworkflow
+
+- job: v1.0/docker-array-secondaryfiles-job.json
+  output: {
+    "bai_list": {
+        "checksum": "sha1$081fc0e57d6efa5f75eeb237aab1d04031132be6",
+        "location": "fai.list",
+        "class": "File",
+        "size": 386
+    }
+  }
+  tool: v1.0/docker-array-secondaryfiles.cwl
+  doc: Test secondaryFiles on array of files.
+
+- job: v1.0/dir7.yml
+  output: {
+    "dir": {
+        "location": "a_directory",
+        "class": "Directory",
+        "listing": [
+            {
+                "class": "File",
+                "location": "whale.txt",
+                "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
+                "size": 1111
+            },
+            {
+                "class": "File",
+                "location": "hello.txt",
+                "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
+                "size": 13
+            }
+        ]
+    }
+  }
+  tool: v1.0/dir7.cwl
+  doc: Test directory literal output created by ExpressionTool
+
+- job: v1.0/empty.json
+  output:
+    lit:
+      location: "a_file"
+      class: "File"
+      checksum: "sha1$fea23663b9c8ed71968f86415b5ec091bb111448"
+      size: 19
+  tool: v1.0/file-literal-ex.cwl
+  doc: Test file literal output created by ExpressionTool
+
+- job: v1.0/empty.json
+  output:
+    "thing": {
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "location": "thing",
+        "class": "File",
+        "size": 0
+    }
+  tool: v1.0/docker-output-dir.cwl
+  doc: Test dockerOutputDirectory
diff --git a/v1.0/salad/README.rst b/v1.0/salad/README.rst
@@ -70,6 +70,6 @@ provides for robust support of inline documentation.
 .. _JSON-LD: http://json-ld.org
 .. _Avro: http://avro.apache.org
 .. _metaschema: https://github.com/common-workflow-language/schema_salad/blob/master/schema_salad/metaschema/metaschema.yml
-.. _specification: http://www.commonwl.org/draft-3/SchemaSalad.html
-.. _Language: https://github.com/common-workflow-language/common-workflow-language/blob/master/draft-3/CommandLineTool.yml
+.. _specification: http://www.commonwl.org/v1.0/SchemaSalad.html
+.. _Language: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/CommandLineTool.yml
 .. _RDF: https://www.w3.org/RDF/