Hey Jun, Like Jen mentioned, you should use multiple output elements if at all possible. The format for specifying outputs you are describing should only be used if the tool does not know the number of outputs to be used prior to execution of the tool. I believe it is a known limitation of this mechanism multiple output mechanism that such tools cannot be used in workflows - many scientific workflow platforms more sophisticated than Galaxy cannot handle such tools - it is hard to reason about workflows without knowledge of their structure ahead of time. That said, there is an open and high priority Trello card outlining dataset collections that will hopefully provide some more robust alternatives to address use cases currently addressed with this multiple output mechanism - https://trello.com/c/325AXIEr. -John On Fri, Nov 8, 2013 at 8:47 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hi Fan,

The <outputs> </outputs> block should contain one line for each of the output files. I believe that you need to name these differently. "output1", "output2", etc. Or you can add in text and use variables, if you add in the " label" option.

Others can correct or add to my comments.

Good luck!

Jen Galaxy team

On 11/8/13 5:41 PM, Jun Fan wrote:

Hi Jen

Thanks for your reply. Yes, it is my own tool.

The outputs element is

<outputs>

<data format="gff3" name="output"/>

</outputs>

In the command element, the three output files are defined as below

$output /$__new_file_path__/primary_${output.id}_samWithPeptides_visible_sam /$__new_file_path__/primary_${output.id}_longestORFs_visible_fasta

Is there anything wrong here?

Best regards!

Jun

*From:* Jennifer Jackson [mailto:jen@bx.psu.edu <jen@bx.psu.edu>] *Sent:* 09 November 2013 01:05 *To:* Galaxy Dev *Cc:* Jun Fan *Subject:* multiple output tool in workflow

Hi Jun,

There is probably a problem with the tool design itself, but that may be what you are asking how to solve. I wouldn't think this is a problem with workflows at first pass.

Is this your own tool? Or a tool from the tool shed (the repo developer is usually the one to make changes, unless you want to try)? This is the primary tool development wiki, the " <output> tag set" is where I would double check the tool first. http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

I am moving this over to the galaxy-dev@bx.psu.edu mailing list since it is a tool development question.

Jen Galaxy team

On 11/8/13 10:19 AM, Jun Fan wrote:

Hi all,

I am trying to creating a workflow from history. One of the tool used generates multiple outputs in the format of gff3, fasta and sam. Gff3 will be visualized in IGV and the fasta file is doing further BLAST analysis. Now the problem is that the automatically generated workflow does not connect the having-multiple-output tool and the BLAST tool. I failed even I tried to connect these two tools in the workflow by hand. I am guessing this is due to only the main output type (gff3) is recognized in the workflow. How could I solve this problem?

Best regards and have a nice weekend!

Jun

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