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

> On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster <g...@bx.psu.edu> 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
name    description     version requirements
hmmpress        Compress profile db     1.0.0   none
Invalid tools - click the tool config file name to see why the tool is invalid
hmmer.xml



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


Repository Actions
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)
Query:
Sequence (i.e. hmmscan)
Profile (i.e. hmmsearch)
Sequences:

[--acc] Prefer accessions over names in output:

[--noali] Omit the alignment section from the main output:

This can greatly reduce the output volume
[--incE] Use an E-value of <= this value as the per-target inclusion threshold:

The default is 0.01, meaning that on average, about 1 false positive would be 
expected in every 100 searches with different query subsequences.
[--incdomE] Use a conditional E-value of <= this value as the per-domain 
inclusion threshold, in targets that have already satisfied the overall 
per-target inclusion threshold:

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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