On 28/05/2010 11:35, Sébastien 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
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