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.


Greg Von Kuster

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,

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?



P.S. Edward, hmmpress.xml is missing hmmpress as a requirement.
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