SRA-tools FASTQ dump fails when using a file list

and selecting `apply left and right clips` or `Dump only biological reads` for certain identifiers.

Example, have a file that contains this identifier `SRR042817`. These are single ended reads, and the error occurs whether or not I set `split spot by read pairs` to true or false

results in this error / traceback

```
galaxy.tools.parameters.output_collect DEBUG 2016-09-28 12:32:03,946 (1697) Created dynamic collection dataset for path [/galaxy/database/jobs_directory/001/1697/working/SRR042817_4.fastq] with element identifier [SRR042817:4] for output [list_paired] (1695.361 ms)
galaxy.tools.parameters.output_collect DEBUG 2016-09-28 12:32:04,339 (1697) Add dynamic collection datsets to history for output [list_paired] (393.093 ms)
galaxy.tools.parameters.output_collect ERROR 2016-09-28 12:32:04,369 Problem gathering output collection.
Traceback (most recent call last):
File "/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 65, in collect_dynamic_collections
collection_builder.populate()
File "/galaxy/lib/galaxy/dataset_collections/builder.py", line 87, in populate
elements = self.build_elements()
File "/galaxy/lib/galaxy/dataset_collections/builder.py", line 58, in build_elements
new_elements[identifier] = element.build()
File "/galaxy/lib/galaxy/dataset_collections/builder.py", line 64, in build
collection = build_collection( type_plugin, self.build_elements() )
File "/galaxy/lib/galaxy/dataset_collections/builder.py", line 12, in build_collection
set_collection_elements( dataset_collection, type, dataset_instances )
File "/galaxy/lib/galaxy/dataset_collections/builder.py", line 19, in set_collection_elements
for element in type.generate_elements( dataset_instances ):
File "/galaxy/lib/galaxy/dataset_collections/types/paired.py", line 24, in generate_elements
self._validation_failed( INVALID_IDENTIFIERS_MESSAGE )
File "/galaxy/lib/galaxy/dataset_collections/types/__init__.py", line 23, in _validation_failed
raise exceptions.ObjectAttributeInvalidException( message )
ObjectAttributeInvalidException: Paired instance must define 'forward' and 'reverse' datasets .
```

Worse yet, I end up with an empty green 'single-end fasta|q' list and a forever "running" yellow 'Paired end fastq' list. No user feedback is available.