Thank you Eric,
But I want to be clear after spending 5 days, reading many Galaxy wiki links, looking at samples, and with help from others trying to get this to work.  I have written many tools but never tried to display a unique datatype before.
Below is a series of questions and steps I followed trying the suggestions from early posts. 
My goals are:
-- To get  the visualization icon to show in the bottom left of my history output file?    
-- click the visualization icon to display my data (that I will process to display) inside Galaxy.
The steps below are in order of urgency:)
Thank you for you patience.
1.  /Config/plugin/visualization is where code goes to have a Galaxy internal module display a user defined data type?  -- mine is binary
Without getting to in the weeds under this directory I have a mydatatype dir with subdirectories /config w xml, /static w .js, /templates w mako made of html
2.  Under /lib/galaxy/datatypes/display_applications  I tried the same approach with no success. Is this where code goes for external displays that use get and post reside?
3.  which if any of 1or2 above use the Tools/Visualization directory.  Is that the convention for the return of a Get or Post external displays?
4.  I create my own datatype in  data_config_type.xml  with a <datatype> tag
5.  in data_config_type.xml you only use the <display>  record which -- internal or external displays?
6.  I added a class in the  file with the name of my new datatype.  
7.  I added a tool.mydatatype section and file with my xml to input and then output my datatype by specifying  format=mydatatype not format=binary.mydatatype       Plus I added this into Tools_conf.xml  Are there other xml specific items I need in my tool xml for an internal visualization
8. By clicking the visualization icon. what does it call (hopefully 1or2 above) so i can add specific code to display my datatype internal "visualization?" (preferred) in galaxy?
----- Original Message -----
From: Eric Rasche <>
Cc: galaxy-dev <>
Sent: Tue, 08 Dec 2015 02:34:47 -0000 (UTC)
Subject: Re: [galaxy-dev] How does one run Javascript or HTML as a tool?
Hi Bob,

Yes, galaxy supports output formats of HTML+JS, though the tool producing them may need to be whitelisted (grep for 'whitelist' in your galaxy.ini) for display to work properly.

If you wish to write your own visualization plugin for a specific datatype, there are assorted pieces of documentation on the wiki that might help you (though I usually just look at one of the other existing visualization plugins and copy+paste).



2015-12-07 20:08 GMT-06:00 <>:
Good evening Galaxy team,
Is it possible to run JavaScript or HTML as a tool or a display module? 
I see support for URLs, e.g. UCSC Genome Browser, but I would like to process a specific datatype to allow it to be viewed in Galaxy -- but the application is a combination of HTML and JavaScript.  
Does Galaxy support this?  
Thank you,


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Eric Rasche
Programmer II
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843