Hi Brent,

I've encountered this behavior too.  I don't know the ultimate reason or 
purpose, but compressed files (especially zip) are handled in very specific, 
restricted ways by the upload framework.  The behavior you describe is hard 
coded into the upload tool.

For example, check out the use of the 'zipfile' module in 
tools/data_source/upload.py.  That file (tool) will actually try to sniff your 
file even if you've set the file type in upload.  See the data flow (or data 
non-flow) through local variable 'ext' in 
tools/data_source/upload.py:add_file().  Odd and restrictive policy for 
treatment of compressed files can be seen elsewhere in the codebase too, 
including test/base/twilltestcase.py:TwillTestCase.verify_dataset_correctness().

My advice (and this is also basically the advice Nate gave me) is to fork your 
own copy of the upload tool to make a version that works for your files.

Nate may have more to say on the matter.

Best,
Eric

________________________________________
From: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Brent Pedersen 
[bpede...@gmail.com]
Sent: Friday, September 30, 2011 11:59 AM
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] upload zip file to custom tool

Hi,
I have followed the wiki and built a custom tool on a local galaxy installation.
One of the inputs is a zip file. It seems galaxy automatically unpacks
it and keeps only
the first file. Is there any way I can tell galaxy not to unzip the file?
I tried to register .zip as a datatype, but that didn't seem to change
the behavior.

thanks for any help.
$tool.xml is below in case it helps.
-Brent

 <command interpreter="python">charmqc.py $xyszip $output $organism</command>
 <inputs>
   <param format="xys.zip" name="xyszip" type="data" label="Zip of
.xys files"/>
   <param type="select" name="organism" label="organism">
       <option value="Human">Human (hg18)</option>
       <option value="Mouse">Mouse (mm8)</option>
    </param>
 </inputs>
 <outputs>
   <data format="data" name="output" />
 </outputs>
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