Implement More Linting

[jmchilton]

• [ ] Certain parameters types require default values, these should be validated.
• [ ] Check test data files exist.
• [ ] Check tests test something (raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or md5 tests, etc...)"))
• [ ] Ensure supplied test parameters reference inputs.
• [x] Compile RST in Help ensure compiles cleanly.
• [ ] Check datatypes (requires a target Galaxy and tool shed) https://github.com/galaxyproject/planemo/issues/678
• [ ] Flag a warning if force_history_refresh is enabled. https://github.com/galaxyproject/tools-iuc/pull/80#discussion_r27023809

[peterjc]

While thinking about #529 I was thinking about things planemo lint could check:

• [ ] All input parameters used in at least one test [warning level]
• [ ] All input parameters used in <command> or <configfile> tags [error level]
• [ ] All named outputs used <command> or <configfile> tags [error level]
• [ ] Check both states of a boolean parameter are used in test [too stringent?]
• [ ] For multiple-selection parameters, check this is used in test [too stringent?]
• [ ] Report warnings in <help> text RST (basic validation already done) [warning level]

Given the linting code is in https://github.com/galaxyproject/galaxy-lib/tree/master/galaxy/tools/linters should I file issues there?

[peterjc]

I think "Check tests test something" can be ticked via https://github.com/galaxyproject/galaxy-lib/blob/master/galaxy/tools/linters/tests.py