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 <jduddy@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.****
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*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****
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*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?****
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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. ****