The BWA tool in NGS mapping does just what you want, just for inputs. The 
general idea is to use a <conditional> element and define your extra output in 
a <when> block.

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584

[] On Behalf Of Nikhil Joshi
Sent: Friday, August 26, 2011 3:57 PM
Subject: [galaxy-dev] outputting different numbers of files based on variables?

Hi all,

Is it possible to output a different number of files based on variables that 
the use has chosen?  I have a program that will output different numbers of 
files based upon the input data.  So, for example, if the user wants to use a 
single-end fastq file, the program outputs only one file, however, if the user 
chooses paired-end fastq files, it outputs three files.  Is there any way to 
get that to work in just one tool?  I could make separate tools for single vs. 
paired end, but I'd rather not.

- Nik.
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