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@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@googlemail.com>wrote:
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@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