soaplab-users

[Soaplab-users] Dependent parameters & parameter value variable in ACD

[Sebastien M. <Seb...@un...>]

Hi,

I have two questions about parameter value variable in ACD syntax.

First, may I use something like
	string: seq [
         	standard: "Y" #Mandatory parameter
         	knowntype: "string"
		minlength: ${min}
	...]
where min is
	integer: min [
         	minimum: 14
         	maximum: 26
         	default: 17
	...]
?


Second, I have two dependent parameters, min and max.
I always want min >= max but their range values are overlapping.
So, is there a way to reject query, from ACD syntax, when max > min ?

Thanks

-- 
Sébastien Moretti

Re: [Soaplab-users] Dependent parameters & parameter value variable in ACD

[Mahmut U. <ul...@eb...>]

Hi Sebastian,

> I have two questions about parameter value variable in ACD syntax.
> 
> First, may I use something like
> 	string: seq [
>          	standard: "Y" #Mandatory parameter
>          	knowntype: "string"
> 		minlength: ${min}
> 	...]
> where min is
> 	integer: min [
>          	minimum: 14
>          	maximum: 26
>          	default: 17
> 	...]
> ?

Although EMBOSS supports the minlength option for the string objects
current Soaplab doesn't support it. If your command line applications
are implemented using EMBOSS framework then EMBOSS checks on run-time
whether the input string lengths have the minimum length specified by
the minlength option.

You can have something similar to the above example using EMBOSS but you
should make sure that in the ACD file you define the referenced options
before the option that refers them. Also instead of curly brackets
EMBOSS use parenthesis when referring to a variable value.

In summary, current Soaplab doesn't have minlength and maxlength
validation for String objects but you can do this validation in your
executable. I don't know whether your Soaplab services are for existing
applications or you are implementing new applications but if you are
writing new bioinformatics applications using C/C++ then you may use
EMBOSS framework to implement them, then you would have this type of
validation at no extra cost.

Regards,
Mahmut
 

Re: [Soaplab-users] Dependent parameters & parameter value variable in ACD

[Sebastien M. <Seb...@un...>]

> Hi Sebastian,
> 
>> I have two questions about parameter value variable in ACD syntax.
>>
>> First, may I use something like
>> 	string: seq [
>>          	standard: "Y" #Mandatory parameter
>>          	knowntype: "string"
>> 		minlength: ${min}
>> 	...]
>> where min is
>> 	integer: min [
>>          	minimum: 14
>>          	maximum: 26
>>          	default: 17
>> 	...]
>> ?
> 
> Although EMBOSS supports the minlength option for the string objects
> current Soaplab doesn't support it. If your command line applications
> are implemented using EMBOSS framework then EMBOSS checks on run-time
> whether the input string lengths have the minimum length specified by
> the minlength option.
> 
> You can have something similar to the above example using EMBOSS but you
> should make sure that in the ACD file you define the referenced options
> before the option that refers them. Also instead of curly brackets
> EMBOSS use parenthesis when referring to a variable value.
> 
> In summary, current Soaplab doesn't have minlength and maxlength
> validation for String objects but you can do this validation in your
> executable. I don't know whether your Soaplab services are for existing
> applications or you are implementing new applications but if you are
> writing new bioinformatics applications using C/C++ then you may use
> EMBOSS framework to implement them, then you would have this type of
> validation at no extra cost.
> 
> Regards,
> Mahmut

OK
I always check this in my application but I wondered if I could check
parameter values before.

Thanks

-- 
Sébastien Moretti