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 E-mail: jduddy@illumina.com<mailto:jduddy@illumina.com> From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nikhil Joshi Sent: Friday, August 26, 2011 3:57 PM To: galaxy-dev@lists.bx.psu.edu 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.