Missing tool previews in tool shed, e.g. hmmer.xml
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.
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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster <greg@bx.psu.edu> 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
On Mar 19, 2012, at 9:34 AM, Peter Cock wrote:
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster <greg@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
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster <greg@bx.psu.edu> 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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Greg Von Kuster -
Peter Cock