Re: [Jstyx-users] Styx

[Jon B. <jd...@ma...>]

Dear Els,

This is a good question.  Currently the SGS software uses the Java
Simple Argument Parser (JSAP, http://www.martiansoftware.com/jsap/) to
parse command-line arguments.  As far as I know, JSAP does not allow
for flags of the form "-sequence".  I will try to find out more from
the JSAP developers.

In the meantime all I can think of is to create a script that wraps
EMBOSS.  The script could accept arguments of the form "--sequence"
and simply replace them with "-sequence".  You would then wrap the
script as the Styx Grid Service.

Would this be a satisfactory solution?  I am sorry that this isn't a
very neat way of doing it.

Best wishes,
Jon

On 11/10/06, Els Vanbleu <El...@de...> wrote:
> Hallo!
>
> I have a question concerning Styx Grid Services and writing a
> configuration file for command line tools.
>
> EMBOSS provides a whole bunch of interesting command line tools for
> sequence manipulation.  However they work, at the command line with
> parameters, preceded with solely a single - instead of double --.
>
> E.g. seqret -sequence <filename> -outseq <outputfile>
>
> The GridServices currently only accept as attributes for a parameter a
> single character flag (-o) or a multiple character longFlag (--outseq).
> Can an additional attribute be created to accept the 'inbetween' Flag
> (-outseq), i.e. a multiple character flag?
>
> Or is there any other easy solution to circumvent this problem?
>
> Thanks in advance!
> Greetz
> Els Vanbleu
>
>
>
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