Hi all, This is something I was recently talking to Bjoern about, and which I'm pretty sure came up at the GCC2013 too, perhaps in the Tool Developer's BoF chat?: http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers
Currently Galaxy Tools should have test data for their functional tests, included in the Tool Shed repository under a test-data folder. That is good. Currently Galaxy Workflows do NOT support similar functional tests and they should (i.e. they need something very similar with a test-data folder and configuration file giving the input/output files and other input parameters). This might make sense as part of any ongoing work to present a workflow within Galaxy as a Tool? Trello issue filed: https://trello.com/c/S5CZGOb3/1061-workflows-need-functional-tests-like-we-have-for-tools Neither Galaxy Tools nor Galaxy Workflows yet have any support for "sample data", which might just be larger examples then we already have for the tool's functional tests. This could even be implemented as and extension to the existing <test> markup where a test can be marked as also being sample data? I am imaging that each tool (and workflow) should have at least one sample input dataset (files and parameters) with a description. These would be shown via new GUI element in the Galaxy interface to auto-populate the Galaxy Tool interface with those sample input files (imported into the current history?) and the associated parameter values - ready for the user to modify if desired and then execute. Ross brought this up sample data for tools back in May 2010, and there is a relevant Trello issue filed: https://trello.com/c/GTLNlcwH/298-308-demystifying-the-first-ever-galaxy-login-experience-make-tools-offer-test-data-if-empty-history In the short term, we can just resort to documenting examples in the Tool's <help> text using URLs to public datasets. Here it would be nice if the workflows also supported a similar <help> field to be shown to the user when running a workflow: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014479.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016132.html https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-rich-text-with-markup Unless enhancing the workflow annotation with a tool <help> like field is imminent, then for workflows we are probably for the short term restricted to documenting sample data in a README file which would be visible on the Tool Shed, but not available once the workflow is actually installed into a Galaxy instance. The current situation is clearly not ideal - what is realistic to hope/aim for in the next Galaxy release? Thanks, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
