Improve experience using cwltool.factory

Issue courtesy @dtitov https://gitter.im/common-workflow-language/common-workflow-language?at=5a0c294ddf09362e670f44bd

> I'm trying to use cwltool from within Python (as a library) to programatically execute CWL tools.
> So I've followed the instructions from GitHub page:
```
import cwltool.factory
fac = cwltool.factory.Factory()

echo = f.make("echo.cwl")
result = echo(inp="foo")
```

> It needs two clarifications:
> - For the Docker-based tools one needs to manually set flag use_container or it will fail.
> - One needs to specify outputs and stderr in CWL-file in order to make it work (which is not required for running in stand-alone mode).

We can improve this in multiple ways, both should happen
- [x] Updating https://github.com/common-workflow-language/cwltool/blob/master/cwltool/main.py#L59
- [ ] Updating the relevant docstrings