Hi Yan,
To see the tools available to work with GFF and GTF datafiles, please see the tool group "Filter and Sort". Galaxy does not have a GFF->GFF3 converter - and I do not know of one. There is a GTF->GFF3 converter in the Tool Shed (details below).
First, you will want to make sure that you actually have GFF and not GTF (GFF is a much older format). http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF
Next, GFF/GTF/GFF3 data can vary quite a bit, even those files that meet the official format specifications. Also, not all would contain the data needed by another if a conversion were to be done (additional files would be required or a different set of related starting files would be needed). Still, there are some tools available to convert GTF->GFF3. For example, you could try a local install (http://getgalaxy.org) with the repository from the Tool Shed named fml_gff3togtf containing a GTF_to_GFF3 tool.
A search with the term "convert GFF to GFF3" will bring up some discussion at several bio chat sites about the issues with doing this, along with other options and an online tool to do the same. How any of these will function with your particular data and the final use (RNA-seq pipeline?) is difficult to predict. Much depends on the inputs.
The best choice is to locate a file that has been already created or that can be extracted from a public database using the tools that they provide. Once you have a file in the appropriate format, the next step is to make certain that the file contains the data the tools needs to perform the calculations you are most interested in. The tool documentation (link to manual) will explain expected inputs vs the output. For GTF/GFF3 data, these data are often in the 9th field.
Conversion can be tricky, but you will likely find a method. The 'usable for gene annotation' portion of your question is more complicated to address and will likely take some testing on your part to see what works and what doesn't (to produce the expected results), but hopefully this gives you some ideas about how to start.
Take care,
Jen Galaxy team
On 8/19/12 6:05 PM, Yan He wrote:
Hello,
I have a .gff file available. Is there a tool in Galaxy to change .gff file to .gff3 to make it usable for gene annotation? Thanks!
Yan
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