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 <mailto: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 <tel:858-736-3584>
    E-mail: jdu...@illumina.com <mailto:jdu...@illumina.com>

    *From:*galaxy-dev-boun...@lists.bx.psu.edu
    <mailto:galaxy-dev-boun...@lists.bx.psu.edu>
    [mailto: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 <mailto: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.



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