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 <eskirton(a)lbl.gov> wrote:
great suggestion; i'll make those changes
On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock(a)googlemail.com>wrote:
> On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton(a)lbl.gov> wrote:
> > hi, peter - i will fix the description and upload hmmsearch and infernal
> > today.
> 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.