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] 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.edumailto: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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson