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 binary.py  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 <e...@tamu.edu>To: 
rbrown1422@comcast.netCc: galaxy-dev <galaxy-...@lists.bx.psu.edu>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).


Cheers,
Eric

2015-12-07 20:08 GMT-06:00 <rbrown1...@comcast.net>:

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,
Bob
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-- 




Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu







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