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(a)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(a)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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jacksonhttp://galaxyproject.org ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/