Specifying stdin using an expression causes filemapper error

``` cwl
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

baseCommand: ['cat']

stdin: $(inputs.input_file.basename)
inputs:
input_file:
type: File

outputs: []
```

On macOS & Linux:

```
(base) mdb-ml:cwltool mdb$ cwltool tmp.cwl --input_file README.rst
/Users/mdb/miniconda3/bin/cwltool 1.0.20181210073803
Resolved 'tmp.cwl' to 'file:///Users/mdb/work/cwltool/tmp.cwl'
[job tmp.cwl] /private/tmp/docker_tmpeknwy5b4$ cat < README.rst
[job tmp.cwl] Job error:
README.rst missing from pathmapper
[job tmp.cwl] completed permanentFail
{}
Final process status is permanentFail
```