This has been confusing for me  also. Perhaps if we had a way to distinguish between<br>the two by prefixing the tool version of a wrapper with &quot;w0.0.5&quot; and the actual tool version with &quot;v1.3.0&quot;?<br>I think that Galaxy determines the versions of the tools it loads at startup in lib/galaxy/tools/__init__.py ToolBox::__add_tool_to_tool_panel()<br>
<br>- log.debug( &quot;Loaded tool id: %s, version: %s into tool panel.&quot; % ( <a href="http://tool.id">tool.id</a>, tool.version ) ) - <br><br>Also check out class Tool which is in the same file...probably requires a bit more code reading to fully understand the underlying<br>
layers in question...<br><br><div class="gmail_quote">On Tue, Dec 11, 2012 at 6:43 PM, Clare Sloggett <span dir="ltr">&lt;<a href="mailto:sloc@unimelb.edu.au" target="_blank">sloc@unimelb.edu.au</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi guys,<br>
<br>
I wasn&#39;t sure if I should send this one to galaxy-user. I have just<br>
confused myself about the versions of tools displayed within Galaxy.<br>
<br>
If I select the TopHat tool, the tool UI says &quot;Tophat for Illumina<br>
(version 1.5.0)&quot;.<br>
After I have run the job, the step panel in the History window says<br>
&quot;Info: TopHat v1.4.1&quot;<br>
<br>
If I select the Cufflinks tool, the tool UI says &quot;Cufflinks (version 0.0.5)&quot;<br>
After running the job, the step panel says &quot;Info: cufflinks v1.3.0&quot;.<br>
<br>
Looking at the xml files, it does look like the version displayed<br>
before running is the wrapper and the version displayed on the<br>
resulting dataset is that of the command-line tool.<br>
<br>
&lt;tool id=&quot;tophat&quot; name=&quot;Tophat for Illumina&quot; version=&quot;1.5.0&quot;&gt;<br>
    &lt;!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 --&gt;<br>
<br>
&lt;tool id=&quot;cufflinks&quot; name=&quot;Cufflinks&quot; version=&quot;0.0.5&quot;&gt;<br>
    &lt;!-- Wrapper supports Cufflinks versions v1.3.0 and newer --&gt;<br>
<br>
So looking at the XML it&#39;s very clear, but from the versions displayed<br>
in Galaxy I was completely confused, particularly since the two tophat<br>
version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we<br>
should change it so that when Galaxy says &quot;version&quot; it is always<br>
explicit about whether it&#39;s &quot;wrapper version&quot; or just &quot;version&quot;?<br>
<br>
It also seems like there&#39;s no way for a user to discover the<br>
command-line tool version without actually running the tool (or is<br>
there)? Is this because Galaxy itself does not know this information?<br>
<br>
All this came about because I&#39;m trying to specify to users which<br>
versions of tools my exported Workflow was built with, and I&#39;m not<br>
sure how to do it without confusing them.<br>
<br>
Thanks,<br>
Clare<br>
<br>
--<br>
<br>
Clare Sloggett<br>
Research Fellow / Bioinformatician<br>
Life Sciences Computation Centre<br>
Victorian Life Sciences Computation Initiative<br>
University of Melbourne, Parkville Campus<br>
187 Grattan Street, Carlton, Melbourne<br>
Victoria 3010, Australia<br>
Ph: 03 903 53357          M: 0414 854 759<br>
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</blockquote></div><br>