incrementing version to 1.25-4, including cwl version in cwl file

Author: briandoconnor

Dockstore.cwl

@@ -3,16 +3,17 @@
 class: CommandLineTool
 id: "BAMStats"
 label: "BAMStats tool"
+cwlVersion: cwl:draft-3
 description: |
     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:1.25-3 > Dockstore.cwl
+    $> dockstore tool cwl --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.25-4 > 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:1.25-3 \
+    $> dockstore tool launch --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.25-4 \
         --json Dockstore.json
     ```
 
@@ -23,8 +24,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25-3"
-  - { import: node-engine.cwl }
+    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25-4"
 
 hints:
   - class: ResourceRequirement
@@ -44,12 +44,14 @@ inputs:
   - 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
 
 outputs:
   - id: "#bamstats_report"
     type: File
+    format: "http://edamontology.org/format_3615"
     outputBinding:
       glob: bamstats_report.zip
     description: "A zip file that contains the HTML report and various graphics."