Shaun,

<version_command> is what you want:

    <version_command>tophat --version</version_command>

A couple things to note:
        *tool path isn't needed if the tool is in your galaxy user's path;
        *your tool must have a --version command line option; if not, you'll 
have to modify the command.

This functionality should be working as of latest Galaxy dist.

If you're still having trouble, it would be useful to try running a tool with a 
known, functioning version command (e.g. Tophat, Bowtie, 
Cufflinks/compare/diff) and seeing if it produces the version as output.

Let us know if you're still having problems.

Thanks,
J.



On Oct 13, 2011, at 5:42 AM, SHAUN WEBB wrote:

> 
> Hi. I am using the tag:
> 
>       <version_string>path to tool --version</version_string>
> 
> In my xml file. I would expect the tool version to be printed in the 
> information window for each dataset but the version field is blank. I am 
> running the latest Galaxy dist, is there anything else I need to do?
> 
> I have tried using <version_command> also.
> 
> Thanks
> Shaun
> 
> 
> 
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