Hi guys,

I wasn't sure if I should send this one to galaxy-user. I have just
confused myself about the versions of tools displayed within Galaxy.

If I select the TopHat tool, the tool UI says "Tophat for Illumina
(version 1.5.0)".
After I have run the job, the step panel in the History window says
"Info: TopHat v1.4.1"

If I select the Cufflinks tool, the tool UI says "Cufflinks (version 0.0.5)"
After running the job, the step panel says "Info: cufflinks v1.3.0".

Looking at the xml files, it does look like the version displayed
before running is the wrapper and the version displayed on the
resulting dataset is that of the command-line tool.

<tool id="tophat" name="Tophat for Illumina" version="1.5.0">
    <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -->

<tool id="cufflinks" name="Cufflinks" version="0.0.5">
    <!-- Wrapper supports Cufflinks versions v1.3.0 and newer -->

So looking at the XML it's very clear, but from the versions displayed
in Galaxy I was completely confused, particularly since the two tophat
version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we
should change it so that when Galaxy says "version" it is always
explicit about whether it's "wrapper version" or just "version"?

It also seems like there's no way for a user to discover the
command-line tool version without actually running the tool (or is
there)? Is this because Galaxy itself does not know this information?

All this came about because I'm trying to specify to users which
versions of tools my exported Workflow was built with, and I'm not
sure how to do it without confusing them.



Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759
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