[EMBOSS] Output files based on input argument
sebastien.moretti at unil.ch
Sat May 29 09:09:59 UTC 2010
I will try this.
>> 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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