Bamtools Filter BAM triggers a combined job instead of distinct jobs with version 2

**Problem**

Multi-select of inputs results in a combined job, instead of distinct jobs, and ends in failure.

**Error** (presumably due to multiple BAM datasets sent as input):

> bamtools filter ERROR: could not open input files for reading.
> /galaxy-repl/main/jobdir/XXX/XXX/XXX/tool_script.sh: line 9: 21396 Segmentation fault (core dumped) bamtools filter -script /galaxy-repl/main/jobdir/XXX/XX/XXX/tmpa1OIsW -in "

**Problem with Galaxy Version 0.0.2
Works correctly with Galaxy Version 0.0.1**

**Example history**

Could be used for testing fix.
https://usegalaxy.org/u/jen/h/test-problem-bamtools--filter-bam-datasets

**Tool v2 details**

- Development repository: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter
- Link to this repository: https://toolshed.g2.bx.psu.edu/view/devteam/bamtools_filter/29ba2103739c

cc @galaxyproject/guac