On Fri, Feb 27, 2015 at 8:58 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
First, hey Peter, thanks for input! I'd seen the explicit piping before, couldn't remember its format though; I will switch to it.
Well, after a morning of testing, I see the test system is actually finding the repeat section variables. It looks like its error "Parameter filter_column requires a value, but has no legal values defined" points to the fact that it can't process any option list having <options from_data_table="[whatever table we got]"> .
I'd assumed Planemo in its test setup would install the tool's data tables, but now I see it is still on John's enhancement list. So I'll table those tests until that's a go.
I guess manually setting up the data tables in galaxy won't solve that for planemo?
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I'm still stuck trying to get tool test directly in a fresh copy of Galaxy. I edit config/tool_conf.xml.sample to have
<section id="testing" name="TESTING"> <tool file="TESTING/blast_reporting/blast_reporting.xml" /> </section>
And I run "tests.sh -id blast_reporting" (with Galaxy as owner of tool folder):
While the tests used to use tool_conf.xml.sample last year (or even longer ago?) this was switched to using the main tool_conf.xml instead. This is much easier for testing what you actually have installed. If I've guessed wrong, watch the run_tests.sh output to see which tools are loaded - and make sure your tool loads OK (and for example doesn't fail with an XML error or something). Peter