Hi,
I'm trying write a Galaxy wrapper for Optimus Primer, http://op.pgx.ca/
Is there any documentation or examples for wrapping web-tools ??
Thanks.
Hi,
I'm trying write a Galaxy wrapper for Optimus Primer, http://op.pgx.ca/
Is there any documentation or examples for wrapping web-tools ??
Thanks.
It is possible but the way it works is very different from the typical tool wrapping. One would need to modify the original web interface so that it knows where to return the results. It works like this:
A sounds a bit complicated but it takes all that. I actually came up with this protocol and implemented this way back many-many years ago, in 2006 most likely, the first source that this worked for was the BioMart. From a cursory examination it seems that this still works this way but I cannot guarantee it since I have not been involved with it for a number of years. See this for more details:
Yes!
These got me started. Once you're familiar with the basics, just dive into the Galaxy files. In the base Galaxy folder, there's a file called "tool_conf.xml" Open that up and you can find paths to tool wrappers. Then you can examine the wrapper of a tool that interests you.
Basically, simple tools can be wrapped with just an XML file. If you need something more sophisticated, you call a script (usually written in python) and pass parameters to it from your XML wrapper. That script constructs the command line for the tool and then executes it. I haven't seen this approach documented, but it's easy enough to figure out if you know a scripting language and take a few minutes to investigate. These secondary scripts are used with Picard and the tuxedo suite, among other tools.
Let me know if you need more info. I've written a ton of wrappers in Galaxy.
Thanks for the reply. I'm looking into a wrapping web-tools such as optimus primer or primer3 (the tool can only be accessed via http, as is not installed in the Galaxy environment), I'd like to know if galaxy is able to handle "get, post" etc. There are a few examples for it, but it seems such webtools support Galaxy access (ratmine, flymine)
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Why would you want to wrap an existing web-based tool? The point of Galaxy is to make command-line tools easier to use by providing a web interface. You already have a web interface.
Yes, your point is valid, although it has been done (flymine, ratmine, etc), I guess the main advantage is to get the web-tool output into Galaxy for further analysis.