Missing tool previews in tool shed, e.g. hmmer.xml

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Missing tool previews in tool shed, e.g. hmmer.xml

Peter Cock
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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Re: Missing tool previews in tool shed, e.g. hmmer.xml

Greg Von Kuster
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



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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Re: Missing tool previews in tool shed, e.g. hmmer.xml

Peter Cock
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster <[hidden email]> wrote:

> 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.

I see - I hope you can make some improvements for browsing the tool
shed for this kind of situation.

Thanks for confirming there was something the Tool Shed didn't like
in hmmer.xml (missing a hmmdb.loc.sample file). For the tool
uploader (in this case Edward) that kind of error is very helpful.

Peter

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Re: Missing tool previews in tool shed, e.g. hmmer.xml

Greg Von Kuster

On Mar 19, 2012, at 9:34 AM, Peter Cock wrote:

On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster <[hidden email]> wrote:

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

I see - I hope you can make some improvements for browsing the tool
shed for this kind of situation.


Invalid tools are now displayed in the "Preview tools and inspect metadata by tool version" section - here is the list for the hmmer repository.


Preview tools and inspect metadata by tool version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
namedescriptionversionrequirements
Compress profile db1.0.0none
Invalid tools - click the tool config file name to see why the tool is invalid


If you click on the invalid tool, the error message is displayed - if the tool can be displayed it is...


This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error.

hmmer (version 1.0.0)
This can greatly reduce the output volume
The default is 0.01, meaning that on average, about 1 false positive would be expected in every 100 searches with different query subsequences.

Note. Hidden Markov Model (HMM) searches take a substantial amount of time. For large input datasets it is advisable to allow overnight processing.


What it does

hmmscan is used to search sequences against collections of profiles. For each sequence in seqfile, use that query sequence to search the target database of profiles in hmmdb, and output ranked lists of the profiles with the most significant matches to the sequence.

hmmsearch is used to search one or more profiles against a sequence database. For each profile in "hmmfile", use that query profile to search the target database of profiles in "seqdb", and output ranked lists of the sequences with the most significant matches to the profile.

If using a user-supplied profile database, it needs to be pressed using hmmpress before it can be searched with hmmscan.

Author

Sean Eddy, Howard Hughes Medical Institute and Dept. of Genetics, Washington University School of Medicine

http://www.genetics.wustl.edu/eddy/

Manual

ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf




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Re: Missing tool previews in tool shed, e.g. hmmer.xml

Peter Cock
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster <[hidden email]> wrote:
>
> Invalid tools are now displayed in the "Preview tools and inspect metadata
> by tool version" section - here is the list for the hmmer repository.
>

Lovely - that will help with the existing tools which are not all
fully compliant with these new requirements :)

Peter
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