[EMBOSS] ACD syntax error for infile

[Sebastien Moretti]

> The error message is, in this case, rather helpful. Just change
> 'standard' to 'parameter'. The rationale for this is that the first
> input file in an ACD file should usually be a 'parameter' to enable
> people to just specify the filename (without qualifier switch) on the
> command line. acdvalid will just give warnings for subsequent files that
> aren't marked as parameters.
> 
> The warnings are just that the first infile is usually has the
> name 'infile' for consistency with other EMBOSS applications.
> You can choose to ignore warnings for local applications.
> 
> So,
> 
>       infile: infile [
>           parameter: "Y"
>           knowntype: "sequence data"
>           prompt: "Name of Sequence (in arbitrary format)"
>           information: "Protein Sequence or Accession number input"
>       ]
> 
> is what acdvalid would prefer.
> 
> HTH
> 
> Alan

Hi Alan,

Thanks,
nevertheless, I cannot use 'parameter: "Y"' because my application 
requires both parameter-name and parameter-value:
	-in=your_file

So, I will try to use the ACD file with the error.

>> Hello,
>>
>> I try to build my own ACD file for one of our application but acdvalid
>> returns a strange error message:
>>
>> Warning: File tmpred.acd line 26: Information string for 'in' not
>> standard 'Sequence file'
>> Error: File tmpred.acd line 26: First input file 'in' is not a parameter
>> Warning: File tmpred.acd line 26: Infile qualifier 'in' is not 'infile'
>> or '*file'(should be 'infile')
>>
>>
>> Here is the problematic section:
>> section: input [
>>      information: "Input section"
>>      type: "page"
>> ]
>>
>>      infile: in [
>>          standard: "Y"
>>          knowntype: "sequence data"
>>          prompt: "Name of Sequence (in arbitrary format)"
>>          information: "Protein Sequence or Accession number input"
>>      ]
>> ...
>>
>> Do you know how to resolve this ?
>> (I use EMBOSS 5.0.0)
>>
>> Thanks

-- 
Sébastien Moretti
SIB, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221