Valid workflow cannot have RDF generated due to lack of urlencoding

## Problem

When running

```
cwltool --validate https://raw.githubusercontent.com/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/workflows/emg-pipeline-v3.cwl
```

The workflow passes validation without issue. However when trying to generate RDF

```
cwltool --print-rdf https://raw.githubusercontent.com/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/workflows/emg-pipeline-v3.cwl
```

```
I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: "https://raw.githubusercontent.com/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/tools/biom-convert-table.yaml#table_type/Function table" does not look like a valid URI, I cannot serialize this as N3/Turtle. Perhaps you wanted to urlencode it?
```

URLs generated by cwltool are not urlencoded before generating the Turtle representation and so an error is thrown. These should be urlencoded or cwltool more restrictive on the types of symbols allowed.

## Workflow Code

[Overall workflow](https://raw.githubusercontent.com/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/workflows/emg-pipeline-v3.cwl)

[Problem file with space in symbols](https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/tools/biom-convert-table.yaml)

## Your Environment
* cwltool version: 1.0.20170622090721