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
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?
----- Original Message -----From: Björn Grüning
<bjoern.gruening(a)gmail.com>To: rbrown1422(a)comcast.net, Eric Rasche
<esr(a)tamu.edu>Cc: galaxy-dev <galaxy-dev(a)lists.bx.psu.edu>Sent: Sat, 12 Dec
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 thatcan 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
5 is missing :)
----- Original Message -----From: Eric Rasche <esr(a)tamu.edu>To:
rbrown1422(a)comcast.netCc: galaxy-dev <galaxy-dev(a)lists.bx.psu.edu>Sent: Tue, 08 Dec
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 <email@example.com>:> > Good evening
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
you,> Bob> ___________________________________________________________> >
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