Merge remote-tracking branch 'origin/master' into remove-empty-baseCo…

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qiukunlong · Jul 20, 2016 · 721ffdc · 721ffdc
2 parents a296c5f + 46ce0c3
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diff --git a/v1.0/CommandLineTool.yml b/v1.0/CommandLineTool.yml
@@ -72,6 +72,7 @@ $graph:
           [error](#stderr) streams as a (streamable) File output.
         * [SoftwareRequirement](#SoftwareRequirement) for describing software
           dependencies of a tool.
+        * The common `description` field has been renamed to `doc`.
 
       ## Errata
 

diff --git a/v1.0/Workflow.yml b/v1.0/Workflow.yml
@@ -38,7 +38,7 @@ $graph:
       This specification represents the first full release from the CWL group.
       Since draft-3, this draft introduces the following changes and additions:
 
-        * The 'inputs' and 'outputs' fields have been renamed 'in' and 'out'.
+        * The `inputs` and `outputs` fields have been renamed `in` and `out`.
         * Syntax simplifcations: denoted by the `map<>` syntax. Example: `in`
           contains a list of items, each with an id. Now one can specify
           a mapping of that identifier to the corresponding
@@ -62,6 +62,7 @@ $graph:
             type: int
             doc: Second input parameter
           ```
+        * The common field 'description` has been renamed to `doc`.
 
       ## Purpose
 

diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml
@@ -771,9 +771,9 @@
 - job: v1.0/stagefile-job.yml
   output: {
     "outfile": {
-        "checksum": "sha1$2d6c5e4430c4b200227cc77d3b0025082505ee19",
-        "size": 1107,
-        "location": "whale.txt",
+        "checksum": "sha1$b769c7b2e316edd4b5eb2d24799b2c1f9d8c86e6",
+        "size": 1111,
+        "location": "bob.txt",
         "class": "File"
     }
   }
@@ -798,4 +798,14 @@
         class: File
         size: 184
   tool: examples/linkfile.cwl
-  doc: The expression in InitialWorkDir listing
+  doc: Test expression in InitialWorkDir listing
+
+- job: v1.0/wc-job.json
+  output:
+    b:
+        checksum: sha1$c4cfd130e7578714e3eef91c1d6d90e0e0b9db3e
+        location: whale.xtx
+        class: File
+        size: 21
+  tool: v1.0/nameroot.cwl
+  doc: Test nameroot/nameext expression in arguments, stdout
diff --git a/v1.0/contrib.md b/v1.0/contrib.md
@@ -5,7 +5,7 @@ Authors:
   project
 * Nebojša Tijanić <nebojsa.tijanic@sbgenomics.com>, Seven Bridges Genomics
 
-Contributers:
+Contributors:
 
 * Brad Chapman <bchapman@hsph.harvard.edu>, Harvard Chan School of Public Health
 * John Chilton <jmchilton@gmail.com>, Galaxy Project, Pennsylvania State University

diff --git a/v1.0/v1.0/nameroot.cwl b/v1.0/v1.0/nameroot.cwl
@@ -0,0 +1,9 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  file1: File
+outputs:
+  b: stdout
+stdout: $(inputs.file1.nameroot).xtx
+baseCommand: []
+arguments: [echo, $(inputs.file1.basename), $(inputs.file1.nameroot), $(inputs.file1.nameext)]
diff --git a/v1.0/v1.0/stagefile.cwl b/v1.0/v1.0/stagefile.cwl
@@ -4,13 +4,20 @@ requirements:
   InitialWorkDirRequirement:
     listing:
       - entry: $(inputs.infile)
+        entryname: bob.txt
         writable: true
 inputs:
   infile: File
 outputs:
   outfile:
     type: File
     outputBinding:
-      glob: $(inputs.infile.basename)
-baseCommand: "sed"
-arguments: ["-i", "s/Ishmael/Bob/", $(inputs.infile.basename)]
+      glob: bob.txt
+baseCommand: "python"
+arguments:
+  - "-c"
+  - |
+    f = open("bob.txt", "r+")
+    f.seek(8)
+    f.write("Bob.    ")
+    f.close()
diff --git a/v1.0/v1.0/template-tool.cwl b/v1.0/v1.0/template-tool.cwl
@@ -2,8 +2,6 @@
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
-  - class: DockerRequirement
-    dockerPull: "debian:8"
   - class: InlineJavascriptRequirement
     expressionLib:
       - { $include: underscore.js }
@@ -12,6 +10,9 @@ requirements:
     listing:
       - entryname: foo.txt
         entry: $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n"))
+hints:
+  DockerRequirement:
+    dockerPull: "debian:8"
 inputs:
   - id: file1
     type: File

diff --git a/v1.0/v1.0/test-cwl-out.cwl b/v1.0/v1.0/test-cwl-out.cwl
@@ -2,8 +2,9 @@ class: CommandLineTool
 cwlVersion: v1.0
 requirements:
   - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: debian:wheezy
+hints:
+  DockerRequirement:
+    dockerPull: "debian:wheezy"
 
 inputs: []