It seems that the <conditional> element can only be used WITHIN a <data>
element in the outputs.  But that won't do what I want.  I know that you can
use <conditional> in the <inputs> element in that way, but it will NOT work
that way in the <outputs> element.  However, I have found a way to do what I
want using the <filter> element.  I basically have all the outputs for both
the single-end and paired-end reads, but I filter out the outputs based on
whether the user chose single or paired end.  If anyone has a better way to
do it, I would love to know!

- Nik.

On Fri, Aug 26, 2011 at 4:26 PM, Duddy, John <> wrote:

>  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:****
> ** **
> *From:* [mailto:
>] *On Behalf Of *Nikhil Joshi
> *Sent:* Friday, August 26, 2011 3:57 PM
> *To:*
> *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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