Interacting with output views in Galaxy
Hi, I was wondering, if anyone could point me to any resources and that allow the user to interact with the view of the output of a tool in Galaxy. So for example, I would like to load an image, draw a region of interest (ROI) (probably via some js routine) and then store that information in a file, generating an input in the History view. This input could then be used for further analysis. I guess Trackster does something like this, but I don't know if its routines are generic enough to handle this type of interaction. Thanks for any info! Steve
Hello, Stephen Although still under initial development, you may want to look into the visualization registry for the infrastructure to render the region and allow the user to interact with it: http://wiki.galaxyproject.org/VisualizationsRegistry http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAb... In a nutshell, it allows you to configure and include a link from the history panel to a custom page that you create with the mako templating system and the javascript you'll need for the interactivity. Galaxy resources (like your initial dataset) are parsed for you and available in the template. For the other half of the problem: creating new data from the interaction of the user, you'll want to look into the tools API (which is what Trackster uses). Still somewhat rough, there have been improvements to it lately that should allow you to run a tool based on user input and keep the chain of reproducibility. Two things to note: 1. I'd recommend not using the upload tool via the API: not because it doesn't work but because adding arbitrary data this way won't be reproducible. 2. Both the visualizations registry and the tools API are still under development. Feel free to contact me on IRC, email, or the mailing lists if you have any trouble though. I hope that helps and let me know if I can provide any more information, Carl On Fri, Nov 29, 2013 at 7:11 AM, Stephen Taylor <stephen.taylor@imm.ox.ac.uk
wrote:
Hi,
I was wondering, if anyone could point me to any resources and that allow the user to interact with the view of the output of a tool in Galaxy. So for example, I would like to load an image, draw a region of interest (ROI) (probably via some js routine) and then store that information in a file, generating an input in the History view. This input could then be used for further analysis.
I guess Trackster does something like this, but I don't know if its routines are generic enough to handle this type of interaction.
Thanks for any info!
Steve
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Hi Carl, Although still under initial development, you may want to look into the visualization registry for the infrastructure to render the region and allow the user to interact with it: http://wiki.galaxyproject.org/VisualizationsRegistry http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAb... In a nutshell, it allows you to configure and include a link from the history panel to a custom page that you create with the mako templating system and the javascript you'll need for the interactivity. Galaxy resources (like your initial dataset) are parsed for you and available in the template. For the other half of the problem: creating new data from the interaction of the user, you'll want to look into the tools API (which is what Trackster uses). Still somewhat rough, there have been improvements to it lately that should allow you to run a tool based on user input and keep the chain of reproducibility. Two things to note: 1. I'd recommend not using the upload tool via the API: not because it doesn't work but because adding arbitrary data this way won't be reproducible. 2. Both the visualizations registry and the tools API are still under development. Feel free to contact me on IRC, email, or the mailing lists if you have any trouble though. I hope that helps and let me know if I can provide any more information, Thanks for the advice above and your kind offer of further help. I will investigate some more. Steve Carl On Fri, Nov 29, 2013 at 7:11 AM, Stephen Taylor <stephen.taylor@imm.ox.ac.uk<mailto:stephen.taylor@imm.ox.ac.uk>> wrote: Hi, I was wondering, if anyone could point me to any resources and that allow the user to interact with the view of the output of a tool in Galaxy. So for example, I would like to load an image, draw a region of interest (ROI) (probably via some js routine) and then store that information in a file, generating an input in the History view. This input could then be used for further analysis. I guess Trackster does something like this, but I don't know if its routines are generic enough to handle this type of interaction. Thanks for any info! Steve ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Carl Eberhard -
Stephen Taylor