fail validation: make-to-cwl/dna.cwl

[jeremiahsavage]

I was looking for an example where the CommandLineTool and Workflow are in one file, and in trying to run
https://github.com/common-workflow-language/workflows/blob/master/workflows/make-to-cwl/dna.cwl
I get:

$ cwltool ~/workflows/workflows/make-to-cwl/dna.cwl 
/home/ubuntu/.virtualenvs/p2_cwl/bin/cwltool 1.0.20160523144113
No cwlVersion found, treating this file as draft-2.
Tool definition failed validation:
While checking object `file:///home/ubuntu/workflows/workflows/make-to-cwl/dna.cwl#rnaseq`
  Field `cwlVersion` contains undefined reference to `https://w3id.org/cwl/cwl#draft-3`
While checking object `file:///home/ubuntu/workflows/workflows/make-to-cwl/dna.cwl#cat`
  Field `cwlVersion` contains undefined reference to `https://w3id.org/cwl/cwl#draft-3`
While checking object `file:///home/ubuntu/workflows/workflows/make-to-cwl/dna.cwl#tr`
  Field `cwlVersion` contains undefined reference to `https://w3id.org/cwl/cwl#draft-3`
While checking object `file:///home/ubuntu/workflows/workflows/make-to-cwl/dna.cwl#main`
  Field `cwlVersion` contains undefined reference to `https://w3id.org/cwl/cwl#draft-3

[cnjr2]

I get the same.

[StarvingMarvin]

@cnjr2, @jeremiahsavage Pull request #95 should fix this issue