In the existing galaxy-central tool XML scripts and the wiki reading I've done I haven't figured out how to get the dataset ID to be used in the hgt.customText URL that will load a particular dataset as a custom track. From http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/... it looks like I would do something like ${my_dataset.qp}, but Cheetah doesn't like that. I'm going off of the URL used as a link from a BED file to the UCSC Genome Browser as follows (ignore the localhost:8081 bit) and just need to fill in the id bit. http%3A%2F%2Flocalhost%3A8081%2Froot%2Fdisplay_as%3Fid%3D1492%26display_app%3Ducsc%26authz_method%3Ddisplay_at. Essentially I'm outputting an HTML file with links to each interval in a file and want to display it at UCSC. -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
Well, after trying the obvious ($param.id), I've got one problem left. When I try to build the URL in my tool XML script, the & are sanitized whether I use & or %2F, etc. Is there are work around for this? In the meantime I'm going to just do a substitution in my perl script. On Mon, Sep 20, 2010 at 4:00 PM, Jesse Erdmann <jerdmann@umn.edu> wrote:
In the existing galaxy-central tool XML scripts and the wiki reading I've done I haven't figured out how to get the dataset ID to be used in the hgt.customText URL that will load a particular dataset as a custom track. From http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/... it looks like I would do something like ${my_dataset.qp}, but Cheetah doesn't like that.
I'm going off of the URL used as a link from a BED file to the UCSC Genome Browser as follows (ignore the localhost:8081 bit) and just need to fill in the id bit. http%3A%2F%2Flocalhost%3A8081%2Froot%2Fdisplay_as%3Fid%3D1492%26display_app%3Ducsc%26authz_method%3Ddisplay_at. Essentially I'm outputting an HTML file with links to each interval in a file and want to display it at UCSC.
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123
jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
Hi Jesse, You can modify the way that Tool parameters are sanitized on a per parameter basis by using the <sanitizer> tag set. This wiki page has more information: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax (search for '<sanititzer> tag set'). It is also possible to turn the sanitization off for an entire tool. Of course, cautiousness is encouraged when modifying the sanitization actions. Thanks for using Galaxy, Dan On Sep 22, 2010, at 10:44 AM, Jesse Erdmann wrote:
Well, after trying the obvious ($param.id), I've got one problem left. When I try to build the URL in my tool XML script, the & are sanitized whether I use & or %2F, etc. Is there are work around for this? In the meantime I'm going to just do a substitution in my perl script.
On Mon, Sep 20, 2010 at 4:00 PM, Jesse Erdmann <jerdmann@umn.edu> wrote:
In the existing galaxy-central tool XML scripts and the wiki reading I've done I haven't figured out how to get the dataset ID to be used in the hgt.customText URL that will load a particular dataset as a custom track. From http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/... it looks like I would do something like ${my_dataset.qp}, but Cheetah doesn't like that.
I'm going off of the URL used as a link from a BED file to the UCSC Genome Browser as follows (ignore the localhost:8081 bit) and just need to fill in the id bit. http%3A%2F%2Flocalhost%3A8081%2Froot%2Fdisplay_as%3Fid%3D1492%26display_app%3Ducsc%26authz_method%3Ddisplay_at. Essentially I'm outputting an HTML file with links to each interval in a file and want to display it at UCSC.
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123
jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123
jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
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