On Tue, Feb 5, 2013 at 4:28 PM, Luobin Yang <yangl...@isu.edu> wrote:
> Hi, Peter,
>
> You are right, I thought there was already a datatype defined for PSSM, but
> it turned out there isn't one yet. I attached a draft tool configuration
> file for psiblast, it was based on the blastp configuration file, please
> revise as you like.
>
> The options that are specific to psiblast are the following:
> 1. num_iterations
> 2. pseudocount
> 3. inclusion_ethresh
>
> Other options should be the same as the blastp program. So a typical command
> line would be the same as blastp except adding above options if non-default
> values are used. I can see there are two optional output files, one is the
> PSSM and the other is ASCII PSSM. Besides using a typical query input,
> psiblast can take a PSSM file or a multiple sequence alignment file as the
> input.
>
> Luobin

Thanks Luobin,

I've checked that into my development repository (on my tools branch):
https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4e9fe67b0f2378494e0

That will allow me to track changes etc as we work on the datatypes.
Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy
Tool Shed.

Regards,

Peter
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