[EMBOSS] Output files based on input argument

Peter Rice pmr at ebi.ac.uk
Fri May 28 16:01:47 UTC 2010

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 

Hope that helps


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