[EMBOSS] Output files based on input argument

[Peter Rice]

On 28/05/2010 11:35, SŽébastien MORETTI wrote:
> Hi
>
> I try to define output section for one of my tool but I cannot find the
> right way:
>
> The tool takes a mandatory argument and returns three different files
> with names starting by the mandatory argument.
> e.g.: input ./tool --pdb=2SRC
> outputs 2SRC.out, 2SRC.gff, 2SRC.bed
>
>
> How to properly code this in ACD format ?

Two choices. The easy way is to get the 2SRC from an input file:

infile: pdb [
     information: "PDB file name"
]

outfile: outfile [
     extension: "out"
]

outfile: gffoutfile [
     extension; "gff"
]

outfile: bedoutfile [
     extension; "bed"
]

This will use the first part of the input file name to make output 
filenames. There is a slight catch that the names will be converted to 
lower case (2src.out 2src.gff 2src.bed)

If you need exactly what you ask for, assuming --pdb is a string, add to 
each outfile definition:

     name: "$(pdb)"

The first part of the name will now default to the value of the --pdb 
qualifier.

Hope that helps

Peter