On Fri, Dec 17, 2010 at 1:11 PM, Daniel Blankenberg wrote:
Hi Peter,
Hi Dan, Thanks for the informative email,
.ext and .extension are actually the same thing (.ext is a readonly @property that returns .extension); this contains the string that Galaxy uses to declare the datatype for a particular instance of a dataset and is also used for the extension for the file when a user clicks the save icon for the dataset in their history.
Do you think it could be added to the wiki page? http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
You are correct that all datasets are stored on disk with a .dat extension. Because the underlying files can actually be set with several different datatypes at a single time (copies of datasets within and between histories, libraries and users, where a user can change the datatype of a history item manually), its not really feasible to have them stored on disk with a more meaningful extension.
I see - you just change the meta data without having to modify the file on disk. That makes good sense.
However, there has been talk in the past about ways to allow the xml for individual tools to specify an actual filename that will be used during tool execution (e.g. using symlinks). This is definitely a worthwhile feature and would, as you suggest, prevent the need for hacks in several wrappers, but I don't think anyone is working on this currently.
There are two cases I can think of here, one is input files where some looks look at the extension (e.g. sam vs bam), the other is output files where the tool doesn't give you any control (e.g. it will use the input filename with another extension). Either would require hacks in the wrapper, so some more flexibility here could be useful in the future. Regards, Peter