common-workflow-language
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diff --git a/‎.travis.yml‎
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diff --git a/‎CITATION‎
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diff --git a/‎README.md‎
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diff --git a/‎draft-3/README.md‎
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diff --git a/‎draft-3/UserGuide.yml‎
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diff --git a/‎draft-3/userguide-intro.md‎
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diff --git a/‎run_test.sh‎
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diff --git a/‎site/cwlsite-draft3-job.json‎
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diff --git a/‎site/cwlsite-job.yaml‎
100644100755
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@@ -0,0 +1,4 @@
+*.txt text eol=lf
+*.fastq text eol=lf
+*.fai text eol=lf
+*.fasta text eol=lf
@@ -0,0 +1,7 @@
+language: python
+python:
+  - 2.7
+before_script:
+  - git clone https://github.com/common-workflow-language/schema_salad.git salad && cd ./salad && pip install . && cd ..
+script:
+  - for target in v1.0/v1.0/*.cwl; do schema-salad-tool ./salad/schema_salad/tests/test_schema/CommonWorkflowLanguage.yml ${target} || exit 1; done
@@ -3,10 +3,11 @@ To cite the Common Workflow Language standard in a publication, please use:
 Amstutz, Peter; Crusoe, Michael R; Tijanić, Nebojša; Chapman, Brad;
 Chilton, John; Heuer, Michael; Kartashov, Andrey; Kern, John; Leehr, Dan;
 Ménager, Hervé; Nedeljkovich, Maya; Scales, Matt; Soiland-Reyes, Stian;
-Stojanovic, Luka (2016): Common Workflow Language, v1.0. figshare.
+Stojanovic, Luka (2016): Common Workflow Language, v1.0. Specification,
+Common Workflow Language working group. https://w3id.org/cwl/v1.0/
 https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 
-@data{common-workflow-language-draft3,
+@data{cwl,
   doi = {10.6084/m9.figshare.3115156.v2},
   url = {http://dx.doi.org/10.6084/m9.figshare.3115156.v2},
   author = {Peter Amstutz; Michael R. Crusoe; Nebojša Tijanić; Brad Chapman;
@@ -15,6 +16,13 @@ Hervé Ménager; Maya Nedeljkovich; Matt Scales; Stian Soiland-Reyes;
 Luka Stojanovic
  },
   publisher = {Figshare},
+  institution = {Common Workflow Language working group},
   title = {Common Workflow Language, v1.0},
   year = {2016}
 }
+
+# Are you editing this file?
+# Synchronize any changes made with
+# README.md
+# and
+# https://github.com/common-workflow-language/user_guide/blob/gh-pages/CITATION
@@ -1,20 +1,23 @@
-# Common Workflow Language Specifications, draft-3
+# Outdated, please refer to CWL version 1.0 specifications
 
-The CWL specifications are divided up into several documents.
+This URL is for the outdated "draft-3" version of the Common Workflow Language standards.
 
-The [User Guide](UserGuide.html) provides a gentle introduction to writing CWL
-command line tools and workflows.
+Please go to https://w3id.org/cwl/ for the latest stable version.
 
-The [Command Line Tool Description Specification](CommandLineTool.html)
+## Common Workflow Language Specifications, draft-3
+
+The CWL draft-3 specifications are divided up into several documents.
+
+The [CWL draft-3 Command Line Tool Description Specification](CommandLineTool.html)
 specifies the document schema and execution semantics for wrapping and
 executing command line tools.
 
-The [Workflow Description Specification](Workflow.html) specifies the document
+The [CWL draft-3 Workflow Description Specification](Workflow.html) specifies the document
 schema and execution semantics for composing workflows from components such as
 command line tools and other workflows.
 
 The
-[Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html)
+[draft-3 version Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html)
 specifies the preprocessing steps that must be applied when loading CWL
 documents and the schema language used to write the above specifications.
 
 
@@ -45,7 +45,7 @@
       class: CommandLineTool
       ```
 
-      The 'cwlVersion` field indicates the version of the CWL spec used by the
+      The `cwlVersion` field indicates the version of the CWL spec used by the
       document.  The `class` field indicates this document describes a command
       line tool.
 
 
@@ -2,27 +2,5 @@
 
 Hello!
 
-This guide will introduce you to writing tool wrappers and workflows using the
-Common Workflow Language (CWL).  This guide describes the current stable
-specification, draft 3.
-
-Note: This document is a work in progress.  Not all features are covered, yet.
-
-<!--ToC-->
-
-# Introduction
-
-CWL is a way to describe command line tools and connect them together to create
-workflows.  Because CWL is a specification and not a specific piece of
-software, tools and workflows described using CWL are portable across a variety
-of platforms that support the CWL standard.
-
-CWL has roots in "make" and many similar tools that determine order of
-execution based on dependencies between tasks.  However unlike "make", CWL
-tasks are isolated and you must be explicit about your inputs and outputs.  The
-benefit of explicitness and isolation are flexibility, portability, and
-scalability: tools and workflows described with CWL can transparently leverage
-technologies such as Docker, be used with CWL implementations from different
-vendors, and is well suited for describing large-scale workflows in cluster,
-cloud and high performance computing environments where tasks are scheduled in
-parallel across many nodes.
+The Common Workflow Language user guide has moved to
+[http://www.commonwl.org/user_guide/](http://www.commonwl.org/user_guide/)
@@ -5,10 +5,24 @@ $(basename $0): Run common workflow tool description language conformance tests.
 
 Syntax:
         $(basename $0) [RUNNER=/path/to/cwl-runner] [DRAFT=cwl-draft-version]
+                       [EXTRA=--optional-arguments-to-cwl-runner]
 
 Options:
-  -nT   Run a specific test.
-  -l    List tests
+  -nT                   Run a specific test.
+  -l                    List tests
+  -jJ                   Specifies the number of tests to run simultaneously
+                        (defaults to one).
+  --only-tools          Only test CommandLineTools
+  --junit-xml=FILENAME  Store results in JUnit XML format using the given
+                        FILENAME
+  --classname=CLASSNAME In the JUnit XML, tag the results with the given
+                        CLASSNAME
+  --verbose             Print the cwltest invocation and pass --verbose to
+                        cwltest
+
+Note:
+  EXTRA is useful for passing --enable-dev to the CWL reference runner:
+  Example: RUNNER=cwltool EXTRA=--enable-dev
 EOF
 
 DRAFT=v1.0
@@ -18,6 +32,8 @@ RUNNER=cwl-runner
 PLATFORM=$(uname -s)
 COVERAGE="python"
 EXTRA=""
+CLASS=""
+VERBOSE=""
 
 while [[ -n "$1" ]]
 do
@@ -31,21 +47,32 @@ do
         -n*)
             TEST_N=$arg
             ;;
+        -j*)
+            TEST_J=$arg
+            ;;
         -l)
             TEST_L=-l
             ;;
         --only-tools)
-            ONLY_TOOLS=--only-tools
+            ONLY_TOOLS=$arg
             ;;
         --junit-xml=*)
             JUNIT_XML=$arg
             ;;
+        --classname=*)
+            CLASS=$arg
+            ;;
+        --verbose)
+            VERBOSE=$arg
+            ;;
         *=*)
             eval $(echo $arg | cut -d= -f1)=\"$(echo $arg | cut -d= -f2-)\"
             ;;
     esac
 done
 
+DRAFT_DIR="$(cd $(dirname $0); pwd)/${DRAFT}"
+
 if ! runner="$(which $RUNNER)" ; then
     echo >&2 "$helpmessage"
     echo >&2
@@ -68,10 +95,13 @@ runtest() {
     "$1" --version
 
     runs=$((runs+1))
-    (cd $DRAFT
-     cwltest --tool "$1" \
-	     --test=conformance_test_${DRAFT}.yaml ${TEST_N} \
-	     ${TEST_L} ${ONLY_TOOLS} ${JUNIT_XML} --basedir ${DRAFT} -- ${EXTRA}
+    (cd $DRAFT_DIR
+     COMMAND="cwltest --tool $1 \
+	     --test=conformance_test_${DRAFT}.yaml ${CLASS} ${TEST_N} \
+	     ${VERBOSE} ${TEST_L} ${TEST_J} ${ONLY_TOOLS} ${JUNIT_XML} \
+	     --basedir ${DRAFT_DIR} -- ${EXTRA}"
+     if [[ $VERBOSE == "--verbose" ]]; then echo ${COMMAND}; fi
+     ${COMMAND}
     )
     checkexit
 }
 
@@ -8,7 +8,8 @@
             "redirect": [],
             "brandlink": "../index.html",
             "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
-            "primtype": null
+            "primtype": null,
+            "extra": { "class": "File", "path": "empty" }
         },
         {
             "source": {
@@ -24,7 +25,8 @@
             "redirect": [],
             "brandlink": "index.html",
             "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
-            "primtype": "#CWLType"
+            "primtype": "#CWLType",
+            "extra": { "class": "File", "path": "empty" }
         },
         {
             "source": {
@@ -43,11 +45,12 @@
                 "https://w3id.org/cwl/cwl#CreateFileRequirement=CommandLineTool.html#CreateFileRequirement",
                 "https://w3id.org/cwl/cwl#EnvVarRequirement=CommandLineTool.html#EnvVarRequirement",
                 "https://w3id.org/cwl/cwl#ShellCommandRequirement=CommandLineTool.html#ShellCommandRequirement",
-                "https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement",
+                "https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement"
             ],
             "brandlink": "index.html",
             "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
-            "primtype": "#CWLType"
+            "primtype": "#CWLType",
+            "extra": { "class": "File", "path": "empty" }
         },
         {
             "source": {$import: draft3-metaschema.json},
@@ -61,15 +64,7 @@
             "redirect": [],
             "brandlink": "index.html",
             "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
-            "primtype": null
-        },
-        {
-            "source": {"$import": "userguide-input.json"},
-            "target": "draft-3/UserGuide.html",
-            "renderlist": [],
-            "redirect": [],
-            "brandlink": "index.html",
-            "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
-            "primtype": null
+            "primtype": null,
+            "extra": { "class": "File", "path": "empty" }
         }
     ]
@@ -1,16 +1,15 @@
 #!/usr/bin/env cwl-runner
-brand: CWL
-brandimg: {class: File, path: CWL-Logo-Header.png}
 cwl:tool: cwlsite.cwl
+brandimg: {class: File, path: CWL-Logo-Header.png}
 render:
-- brandimg: '<img src=''CWL-Logo-Header.png'' style=''height: 61px; margin-top: -20px;
-    margin-left: -20px''></img>'
-  brandlink: index.html
-  primtype: null
-  redirect: []
-  renderlist: []
-  source: {class: File, path: ../README.md}
+- source: {class: File, path: ../README.md}
   target: index.html
+  brandlink: index.html
+  brandimg: '<img src=''CWL-Logo-Header.png'' style=''height: 61px; margin-top: -20px;
+    margin-left: -20px''></img>'
+  extra:  {class: File, path: empty}
+  # renderlist: []
+  # redirect: []
 - {$import: cwlsite-draft3-job.json}
 - {$import: cwlsite-v1.0.0-job.json}
 - {$import: cwlsite-v1.1.0-dev1-job.yaml}