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. Thanks, Clare -- 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