I've been working off of a local instance of Galaxy (6799:40f1816d6857) to 
develop tools and I'm running into some issues which I'm not sure how to 
resolve idiomatically.

First, some of the tools I'm trying to write Galaxy wrappers for take a 
directory as input. The directory contains some metadata and some related files 
(a FASTA alignment; a Newick tree; etc.). Originally I tried making a data type 
that was a .tar.gz'd directory and a converter that would untar it to a 
directory by doing approximately `rm $output; mkdir $output; tar xf $input -C 
$output`. This was causing errors in Galaxy; I can get these if it would be 
useful, but I figured that this is probably an unsupported thing anyway.

The way that I'm handling it now is to untar the archive every time that the 
tool is run, but it seems like there's probably a better way of setting this up.

Second, these tools also expect their inputs to have a meaningful file 
extension, but it seems like the filenames that Galaxy gives to the tool all 
just have ".dat" as the extension. I was getting around this by doing `ln -s 
$input input.ext`, but again, this seems suboptimal. It's also complicated by 
that some of these programs can take a FASTA or Stockholm alignment, but decide 
which parser to use by the extension. I'd like to be able to support both, but 
it seems like that would require somehow getting the file type out of the 
metadata and doing some sort of check against that.

I've seen some mailing list posts that talk about doing the same symlink trick, 
but I'm kind of hoping that there's some better method available now.

Thanks for any insight into writing idiomatic Galaxy tools,

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