Good morning Bjorn,

I accidentally sent the email before I finished. Thanks for the response to q1-4.

The following questions are part of my request.

5. In data_config_type.xml you only use the <display> record which -- manages internal or external displays or both?

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. How does one get the visualization icon to appear in the bottom left of the output file history? Is there something I need to add to the tool xml?

9. By clicking the visualization icon. what does it call so i can add specific code to display my datatype internal "visualization?" (preferred) within galaxy?

thanks

Bob

----- Original Message -----
From: Björn Grüning <bjoern.gruening@gmail.com>
To: rbrown1422@comcast.net, Eric Rasche <esr@tamu.edu>
Cc: galaxy-dev <galaxy-dev@lists.bx.psu.edu>
Sent: Sat, 12 Dec 2015 14:53:56 -0000 (UTC)
Subject: Re: [galaxy-dev] How does one run Javascript or HTML as a tool?

> Thank you Eric,
>
> But I want to be clear after spending 3 days with help from others trying to get this to work.
>
> 1. Config/plugin/visualization is where code goes to have a Galaxy internal module display a user defined data type -- mine is binary

> 2. Datatype/data_applciations is 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 for the return of a Get or Post?

This is a tool. A completely different concept. Tools are entities that
can run one a cluster and can run separated from the user interface.

> 4. I create my own datatype in data_config_type.xml with a <datatype> tag

> ----- Original Message -----From: Eric Rasche <esr@tamu.edu>To: rbrown1422@comcast.netCc: galaxy-dev <galaxy-dev@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 <rbrown1422@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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