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

aa320ec Merge pull request #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 #339 from common-workflow-language/dockerOutputDirectory
4f65d1f Add test for dockerOutputDirectory option of DockerRequirement.
cb1f928 Merge pull request #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 #324 from common-workflow-language/secondaryfiles-array
5e6c2d4 Add NLeSC's Xenon
cbe1c8d Merge pull request #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 #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 #319 from common-workflow-language/test-cwl-out2
ed40737 Add additional test for cwl.output.json behavior.
a217bb6 Merge pull request #317 from StarvingMarvin/master
8dd69f2 fixing test in v1.0 and v1.1.0-dev1
e831c20 Merge pull request #314 from common-workflow-language/test-requirements-on-steps
8cad6f1 Add test for requirements/hints on workflow steps.
7679adb Merge pull request #308 from common-workflow-language/embedded-subworkflow-test
1582677 Tighten up formatting
779c2d4 Add test for embedded subworkflow
e22a9c2 Merge pull request #307 from alaindomissy/patch-3
125cb5f Update UserGuide.yml
99f4f9f Merge pull request #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

Author: mr-c

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
 

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/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."

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.

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