Hi Peter,

Here is the error produced by attempting to load the hmmr.xml tool config into 
the tool shed.  With regard to tool validity, the definition of a valid tool in 
the tool shed has always been restricted to the tool properly loading in a 
Galaxy instance.  If a tool is not valid, it will not be returned in a search 
and it cannot be automatically installed (unless it belongs to a repository 
containing other valid tools).  I'll consider ways to list invalid tools 
contained in repositories in the tool shed, but the preference is for tool 
developers to share only valid tools, or the value of the tool shed will be 
significantly diminished over time.  Filtering out files that actually are not 
tools from a list of invalid tools could become a bit messy.

Thanks,

Greg Von Kuster



Repository Actions
Metadata was defined for some items in revision '66f8262e1686'. Correct the 
following problems if necessary and reset metadata.
hmmer.xml - This file refers to a file named hmmdb.loc. Upload a file named 
hmmdb.loc.sample to the repository to correct this error.


On Mar 19, 2012, at 6:15 AM, Peter Cock wrote:

> Hello all,
> 
> I was looking at Edward's updated HMMER wrapper on the toolshed,
> http://toolshed.g2.bx.psu.edu/
> 
> There is a preview offered for the (simple) hmmpress.xml only, giving
> the impression that Edward's repository isn't very useful.
> 
> Why isn't anything shown for the more complex hmmer.xml? If there
> is a problem rendering the preview, it would still be useful to list the
> tool in the table with its description, version and requirements.
> 
> Edward - I have a query (which might be what the Tool Shed preview
> is unhappy about), where is the "hmmer" file format referenced in
> hmmer.xml defined? In hmmpress.xml  you use "hmm" (as an input)
> and "hmmpressed" (as an output) which are both defined in hmmer.py,
> so is this an accidental inconsistency?
> 
> Thanks,
> 
> Peter
> 
> P.S. Edward, hmmpress.xml is missing hmmpress as a requirement.
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