Thanks for the info.  However, my problem is that the "Tool Version" field is completely empty in my history items (eg. Tophat2, Cuffdiff).  I suppose I can check the dependancies list you described, but it would be important to know precisely which version was run on any given query.  

Best regards,

Cory

Message: 3
Date: Tue, 5 Nov 2013 09:45:19 +0000
From: "graham etherington (TSL)"
        <graham.etherington@sainsbury-laboratory.ac.uk>
To: Cory Dunn <cdunn@ku.edu.tr>, "galaxy-user@bx.psu.edu"
        <galaxy-user@bx.psu.edu>
Subject: Re: [galaxy-user] Cuffdiff version not apparent
Message-ID:
        <CE9E6D0A.21768%graham.etherington@sainsbury-laboratory.ac.uk>
Content-Type: text/plain; charset="Windows-1252"

Hi Cory,
A list of Galaxy dependancies can be found on the wiki at:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
...although many tools allow a range of tool versions.

You can also identify the information about the specific tool versions by
clicking on the View Details ?i? icon of a history item created by that
tool and looking at the Tool Version field.
If you?re using the Galaxy public server (https://usegalaxy.org/) then
clicking on the ?i? icon of a cuffdiff output file will show:

Tool Version:cuffdiff v2.1.1 (4046M)
Hope this helps.

Cheers,
Graham

 

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