Could you send me the traceback and perhaps a copy of the misbehaving tool 
config files?  I'll be happy to take a look.

Thanks!

Dannon


On Nov 21, 2011, at 9:53 AM, Steven Platt wrote:

> A colleague of mine posted this on the Users list ... 4 days later and
> no replies! I'm hoping that one of the Devs can shed a bit of light
> ------------------------------------------------------------------------
> ---------------------------------------------------
> A peculiar bug, presented for your input:
> 
> A colleague has built a few tools and is trying to incorporate them into
> a workflow. However:
> 
> 1.       When he creates an new empty workflow, edits it and adds the
> tools, they appear without inputs (i.e. the icons/boxes on the diagram
> have no input "sockets")
> 2.       When he tries to save a history using these tools as a
> workflow, a error results in which Galaxy complains about an
> unrecognised name, being one of the tool inputs. Depending on which tool
> he includes in the workflow, the missing name occurs in whichever tool
> is earlier in the workflow. (Traceback available on request)
> 
> Puzzling. And even more puzzling when I tried to debug this:
> 1.       Other tools (not written by him) behave in the workflows as
> expected.
> 2.       Pulling a copy of his config file across to my own instance of
> Galaxy and creating a dummy tool to house it, it worked perfectly 
> 3.       We're running the same version of Galaxy, albeit different
> versions of Python (2.5 vs 2.6.4)
> 4.       The tools work fine in normal analysis mode.
> 5.       Line-ending unix, XML seems to parse fine. 
> 
> I'm stymied here and unsure what to look at next. Ideas?
> ------------------------------------------------------------------------
> ---------------------------------------------------
> 
> Thanks
> 
> Steve
> 
> Dr Steven Platt
> Bioinformatician
> Health Protection Agency
> Microbiology Services Division
> London
> www.hpa.org.uk/bioinformatics 
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