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 <jduddy@illumina.com <mailto: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.

*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: jduddy@illumina.com <mailto:jduddy@illumina.com>

*From:*galaxy-dev-bounces@lists.bx.psu.edu <mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto: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 <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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Thanks for the pointer Ross. It was really useful. I also found more information about multiple output datasets on the wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files?highlight=%2... I plan on writing a script that renames the output of the Grinder tool I am wrapping to a name that will work well with what Galaxy expects from multiple output datasets. Best, Florent On 15/09/11 18:44, Ross wrote:

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.angly@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<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.

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

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.