i created a new toolshed repo, hmmer since i couldn't rename it.  as
suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress.  will
add hmmbuild, hmmalign asap; others upon request.

dave, is there a way to delete an old tool?  (hmmscan)

On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton <eskir...@lbl.gov> wrote:

> great suggestion; i'll make those changes
> On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:
>> On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskir...@lbl.gov> wrote:
>> > hi, peter - i will fix the description and upload hmmsearch and infernal
>> > today.
>> Great.
>> Assuming hmmscan and hmmsearch have (almost) the same command
>> line API, there is something to be said for presenting them as one tool
>> in Galaxy, with a drop down selection between them (with help text
>> about which is recommend adapted from the HMMER blog post). One
>> could even have an automatic selection by a wrapper script based on
>> the number of query sequences and the number of HMMs. My thinking
>> here is the detail of hmmscan vs hmmsearch is purely an implementation
>> detail that the end user shouldn't have to worry about.
>> Or just duplicate most of the XML code and have two wrappers. But
>> as far as I know there isn't (yet) a nice way of reusing XML snippets
>> between tool wrappers... which would be handy.
>> Thanks,
>> Peter
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