I hate to reply to my own message, but I could really use some help here.
Is there any way to get the file url within a tool configuration (xml) file?
Thanks!
On 08/26/2010 10:48 AM, Marijn Vandevoorde wrote:
Hi all,
I'm trying to integrate genomeview as a display application. The configuration of the display applications seems to be pretty straightforward, but genomeview needs multiple input files.
I can of course write a cgi file that will take a bunch of get parameters and use these as input files for the java applet. so on the side of genomeview, there's not really a big problem.
however, to integrate it with galaxy, i don't see how to send multiple datasets to genomeview. you can only add the "view with genomeview" link to one dataset (or to all, but all will be viewed seperately).
so i came up with the idea of a new datatype, .gvl, the genomeview list.
in it, basically, a list of links to the datasets, so galaxy can work with them. i could make a tool, gvl creator, to take several datasets as input and then create a really simple textfile containing one url per line, for each dataset.
i think this is the way to go (if anyone has better suggestions, please tell!) but now come the real questions:
most important:
how do i get the public url of my datasets? all other tools use the filesystem path, can't really find an example.
and secondly: any idea how i could maybe take a dynamic number of inputs? i suppose that's not possible. this is not that big a problem. i could combine multiple gvl creators and then a gvl merger or something, no biggie!
all help really appreciated. and of course i'll be happy to share everything with whoever is interested afterwards :-)
with kind regards,
marijn