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:j...@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-...@bx.psu.edu<mailto:galaxy-...@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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