Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?
Good morning Bjorn,
The way I understand Galaxy is worksteps involve a tool using History inputs and creates History output files. I view the results from the tool one click's on the eyeball to see the output file content.
In following this same flow, I was trying to have my datatype display my heatmap when the user clicks on the eyeball after creating the history output file from the HM creation tool.
Similar to how one can display an image file or csv by clicking on the eyeball.
Thanks again, bob
----- Original Message -----From: rbrown1422@comcast.netTo: Björn Grüning bjoern.gruening@gmail.comSent: Sun, 06 Dec 2015 15:49:56 -0000 (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?
Good morning and thanks Bjorn,
One question on your statement ...This does not work with the eyeball, but with the visualization buttonassociated to every dataset. How is this invoked so the dataset is displayed if not by the eyeball?
Let me digest this info and hopefully I can take it from here.
cheers, bob
----- Original Message -----From: Björn Grüning bjoern.gruening@gmail.comTo: rbrown1422@comcast.net, galaxy-dev galaxy-dev@lists.galaxyproject.orgSent: Fri, 04 Dec 2015 18:14:51 -0000 (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?
Hi Bob,
you could write a special visualisation for your specific datatype. Thisdoes not work with the eyeball, but with the visualisation buttonassociated to every dataset.
For a few visualisation examples please see the following links:
*https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizatio... https://github.com/bgruening/galaxytools/tree/master/visualisations* https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook
Hope this gets you started!Bjoern
Good afternoon,> > I am trying create a display module for a special binary datatype.> When someone requests to view the output file in the History using> the eyeball it will kick off my code to create an HTML display in the> Galaxy center section. I am looking at binary.py but I am not sure> if this is it. Is there sample or existing code to look at?> > I hope this makes sense to someone on the team.> > Thanks, bob> > > > ___________________________________________________________ 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: https://lists.galaxyproject.org/%3E > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/%3E
Hi Bob,
Good morning Bjorn,
The way I understand Galaxy is worksteps involve a tool using History inputs and creates History output files. I view the results from the tool one click's on the eyeball to see the output file content.
In following this same flow, I was trying to have my datatype display my heatmap when the user clicks on the eyeball after creating the history output file from the HM creation tool.
So the eyeall is trying to display the real data. If this is an image we render the image, if it's a csv we try to visualise the tabular data.
If you want to visualise your data in a non-standard way, you can write your own visualisations and append them to a specific datatype. For example we added an interactive BAM visualisation.
Have a look at this video, to see a list of visualisations:
https://www.youtube.com/watch?v=jQDyTuYnn1k
Sorry, have not found a better example. IPython is not a real visualisation but uses the same menue.
Cheers, Bjoern
Similar to how one can display an image file or csv by clicking on the eyeball.
Thanks again, bob
----- Original Message -----From: rbrown1422@comcast.netTo: Björn Grüning bjoern.gruening@gmail.comSent: Sun, 06 Dec 2015 15:49:56 -0000 (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?
Good morning and thanks Bjorn,
One question on your statement ...This does not work with the eyeball, but with the visualization buttonassociated to every dataset. How is this invoked so the dataset is displayed if not by the eyeball?
Let me digest this info and hopefully I can take it from here.
cheers, bob
----- Original Message -----From: Björn Grüning bjoern.gruening@gmail.comTo: rbrown1422@comcast.net, galaxy-dev galaxy-dev@lists.galaxyproject.orgSent: Fri, 04 Dec 2015 18:14:51 -0000 (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?
Hi Bob,
you could write a special visualisation for your specific datatype. Thisdoes not work with the eyeball, but with the visualisation buttonassociated to every dataset.
For a few visualisation examples please see the following links:
*https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizatio... https://github.com/bgruening/galaxytools/tree/master/visualisations* https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook
Hope this gets you started!Bjoern
Good afternoon,> > I am trying create a display module for a special binary datatype.> When someone requests to view the output file in the History using> the eyeball it will kick off my code to create an HTML display in the> Galaxy center section. I am looking at binary.py but I am not sure> if this is it. Is there sample or existing code to look at?> > I hope this makes sense to someone on the team.> > Thanks, bob> > > > ___________________________________________________________ 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: https://lists.galaxyproject.org/%3E > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/%3E
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