Prevent no choice in multiple selections.
Fix reference to 'Fetch taxonomic representation' tool.
Fix for "syntax error near unexpected token `;;'".

<command> should not end with a semicolon, otherwise
BaseJobRunner.build_command_line() would create a bash command containing
';;' when appending metadata setting commands.
Refactor building command lines out of job runner base into its own module.
Add unit tests. Test skipping metadata, using metadata, return code patch, dependency shell commands.
Fix bug related to trailing semi-colon in tools.
Thanks to Bjoern, Nicola, Nate for helping track this down.
Restore improvements to job output checking code.
Merge pull request #235.

Fix for tools with trailing semi-colons.
Merged in nsoranzo/galaxy-central-tools2 (pull request #234)

Bug fixes for 3 tools (rebased #222)