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.


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.


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