RE: [Soaplab-users] ACD question

[Marc L. <Mar...@DE...>]

Feels a little strange, answering my own post ;-)

Finally I used this trick:

boolean convert_to_uppercase [
   additional: "Y"
   prompt: "Convert to uppercase"
   default: "false"
   comment: "defaults"
   comment: "method -u"
]

The trick is taking advange of an applab feature and works as such: if a
user passes a value that matches the default value (here set to false)
the option is not passed to the command line. With any other value
different from false (e.g true :-) applab will pass the option '-u' to
the command line.

You can use that trick also for other parameter types but you have to
take care: you should not lie about the default value !!
Because: Suppose you have a blast service and a paramater expect_cutoff
that defaults to 1E-2 (at least, according to the acd file). However,
the blastall default e-value is 10.0.
Meaning, in the acd you actually lied about the real default e-value
that blastall is using. As a consequence, when a user really passes the
value 1E-2 for the expect_cutoff parameter, it matches the default value
and therefor the option is not passed to the blastall command line. As a
result, blastall is run with the real e-value of 10.0 !=20

Hope it will help somebody, some day ...

Cheers,
Marc



> -----Original Message-----
> From: soa...@li...=20
> [mailto:soa...@li...] On Behalf=20
> Of Marc Logghe
> Sent: Thursday, February 23, 2006 4:15 PM
> To: soa...@li...
> Subject: [Soaplab-users] ACD question
>=20
> Hi,
> Suppose you have a command line that takes an option -u (let=20
> say it means uppercase). If '-u' is omitted, it produces lowercase.
> I started off like this:
>=20
> boolean convert_to_uppercase [
>   additional: "Y"
>   prompt: "Convert to uppercase"
>   comment: "method -u"
> ]
>=20
> A soaplab user would see the option 'convert_to_uppercase'.=20
> Internally this is mapped by soaplab to '-u' without a value.
> Problem is, no matter what value is given (true or false)=20
> this option would be put on the command line and this is not=20
> what the user expects.
> Is there a way to make this conditinal ?
> Something like:
>   comment: "method @($$ =3D=3D true ? '-u' : '')
>=20
> I have a terrible feeling I am overlooking something ...
> But any suggestions are welcome.
> Thanks,
> Marc
>=20
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>=20