[17.01] More careful inspection of fixes for MAF tools requiring Galaxy.

[jmchilton]

Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934.

[nsoranzo]

@jmchilton What about the bx imports? It seems to me that all maf tools should have a requirement on bx-python to properly work, especially the ones not on this list.

[jmchilton]

maf_limit_size was removed from the list - its Python file imports are as follows:

from __future__ import print_function

import sys

import bx.align.maf

Since it doesn't import galaxy - I don't think it needs to be in the list. Galaxy's dependencies such as bx are still exposed to tools. A lot more would break I think if bx were to disappear.

[nsoranzo]

I'll investigate the bx-python requirement issue separately.