On Mar 19, 2012, at 9:34 AM, Peter Cock wrote:
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster
> 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
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
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)
Sequence (i.e. hmmscan)
Profile (i.e. hmmsearch)
[--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
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.
Sean Eddy, Howard Hughes Medical Institute and Dept. of Genetics, Washington University
School of Medicine