Merge pull request #1 from briandoconnor/feature/brian_cwl_1

moved to CWL 1.0

Dockstore.cwl

@@ -1,60 +1,77 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-id: "BAMStats"
-label: "BAMStats tool"
-cwlVersion: cwl:draft-3
-description: |
-    ![build_status](https://quay.io/repository/briandoconnor/dockstore-tool-bamstats/status)
-    A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information.
-    ```
-    Usage:
-    # fetch CWL
-    $> dockstore tool cwl --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7 > Dockstore.cwl
-    # make a runtime JSON template and edit it (or use the content of sample_configs.json in this git repo)
-    $> dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
-    # run it locally with the Dockstore CLI
-    $> dockstore tool launch --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7 \
-        --json Dockstore.json
-    ```
+id: BAMStats
+label: BAMStats tool
+cwlVersion: v1.0
+
+$namespaces:
+  dct: http://purl.org/dc/terms/
+  foaf: http://xmlns.com/foaf/0.1/
+  doap: http://usefulinc.com/ns/doap#
+  adms: http://www.w3.org/ns/adms#
+  dcat: http://www.w3.org/ns/dcat#
+
+$schemas:
+- http://dublincore.org/2012/06/14/dcterms.rdf
+- http://xmlns.com/foaf/spec/20140114.rdf
+- http://usefulinc.com/ns/doap#
+- http://www.w3.org/ns/adms#
+- http://www.w3.org/ns/dcat.rdf
+
+doc: |
+  ![build_status](https://quay.io/repository/briandoconnor/dockstore-tool-bamstats/status)
+  A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information.
+  ```
+  Usage:
+  # fetch CWL
+  $> dockstore tool cwl --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7 > Dockstore.cwl
+  # make a runtime JSON template and edit it (or use the content of sample_configs.json in this git repo)
+  $> dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
+  # run it locally with the Dockstore CLI
+  $> dockstore tool launch --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7 \
+      --json Dockstore.json
+  ```
 
 dct:creator:
-  "@id": "http://orcid.org/0000-0002-7681-6415"
+  '@id': http://orcid.org/0000-0002-7681-6415
   foaf:name: Brian O'Connor
-  foaf:mbox: "mailto:briandoconnor@gmail.com"
+  foaf:mbox: mailto:briandoconnor@gmail.com
 
 requirements:
-  - class: DockerRequirement
-    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7"
+- class: DockerRequirement
+  dockerPull: quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7
+- class: InlineJavascriptRequirement
 
 hints:
-  - class: ResourceRequirement
-    coresMin: 1
-    ramMin: 4092
-    outdirMin: 512000
-    description: "the process requires at least 4G of RAM"
+- class: ResourceRequirement
+  coresMin: 1
+  ramMin: 4092
+  outdirMin: 512000
+  description: the process requires at least 4G of RAM
 
 inputs:
-  - id: "#mem_gb"
+  bam_input:
+    type: File
+    format: http://edamontology.org/format_2572
+    inputBinding:
+      position: 2
+    doc: The BAM file used as input, it must be sorted.
+
+  mem_gb:
     type: int
     default: 4
-    description: "The memory, in GB, for the reporting tool"
     inputBinding:
       position: 1
-
-  - id: "#bam_input"
-    type: File
-    description: "The BAM file used as input, it must be sorted."
-    format: "http://edamontology.org/format_2572" 
-    inputBinding:
-      position: 2
+    doc: The memory, in GB, for the reporting tool
 
 outputs:
-  - id: "#bamstats_report"
+  bamstats_report:
     type: File
-    format: "http://edamontology.org/format_3615"
+    format: http://edamontology.org/format_3615
     outputBinding:
       glob: bamstats_report.zip
-    description: "A zip file that contains the HTML report and various graphics."
+    doc: A zip file that contains the HTML report and various graphics.
+
+baseCommand: [bash, /usr/local/bin/bamstats]
 
-baseCommand: ["bash", "/usr/local/bin/bamstats"]

sample_configs.json

@@ -1,10 +1,12 @@
 {
   "bam_input": {
         "class": "File",
+        "format": "http://edamontology.org/format_2572",
         "path": "https://s3.amazonaws.com/oconnor-test-bucket/sample-data/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
     },
     "bamstats_report": {
         "class": "File",
+        "format": "http://edamontology.org/format_3615",
         "path": "/tmp/bamstats_report.zip"
     }
 }

sample_configs.local.json

@@ -1,10 +1,12 @@
 {
   "bam_input": {
         "class": "File",
+        "format": "http://edamontology.org/format_2572",
         "path": "/tmp/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
     },
     "bamstats_report": {
         "class": "File",
+        "format": "http://edamontology.org/format_3615",
         "path": "/tmp/bamstats_report.zip"
     }
 }