Before executing a tool, the Galaxy wrapper version is included in the full tool name at the top of expanded tool form (click on the tool name from the tool panel to "expand" in the center panel). From that same view, a link to the Tool Shed with full tool details is found under the a tool's Options menu.
Once a tool has been executed, the version(s) used (including depedencies and their versions), can be found listed on the "i" info View Details page per-dataset.
For Samtools at http://usegalaxy.org, the View details page will include a section like this, indicating Samtools version 1.3.1 was used during tool execution.
Dependency Dependency Type Version
samtools conda 1.3.1
Hope this helps! Jen, Galaxy team