If you need every output as an item in your history, does the example
in http://lists.bx.psu.edu/pipermail/galaxy-user/2009-September/000743.html
help? Naming might be a wart.
Otherwise the html datatype is really handy for throwing variegated
output into a single history item page. It can look like FastQC eg.

On Thu, Sep 15, 2011 at 5:47 PM, Florent Angly <florent.an...@gmail.com> wrote:
> Hi,
> I too would be interested in knowing how to handle tools that might generate
> multiple output files for the Grinder wrapper I am developing. Any news on
> this? Has a ticket been recorded?
> How about when the tool generate an number of files that cannot be
> determined from the values the user inputs in the form, or when you don't
> know what the files will be named. It seems like there should be generic way
> to loop through the files that were created by the tool in its working
> directory and decide what to do about them.
> Thanks,
> Florent
> On 27/08/11 10:22, Nikhil Joshi wrote:
> 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 <jdu...@illumina.com> 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: jdu...@illumina.com
>> From: galaxy-dev-boun...@lists.bx.psu.edu
>> [mailto:galaxy-dev-boun...@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.

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