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