Hello Siemen,

You'll have to treat Excel files as a specific data type, and add support for 
that data type to Galaxy - see our wiki at 
http://wiki.g2.bx.psu.edu/Admin/Datatypes for details on how to add support for 
a new data type.  You can implement the Excel class in such a way that nothing 
gets munged, which is undoubtedly what is now happening when you upload the 
file because Galaxy sniffs it as some other data type.  

I'm not sure, but perhaps others in the community have done work in this area.

Greg Von Kuster

On Dec 8, 2011, at 4:11 AM, Siemen Sikkema wrote:

> Hello!
> 
> For our future galaxy users in Netherlands Bioinformatics Centre we'd like to 
> support Excel uploads. We have our own excel to tabular CLI tool and I have 
> been trying to get it working with galaxy. The tool itself is not the 
> problem, but getting excel files uploaded is…
> 
> We're running a local instance (hg identify: 949e4f5fa03a+ tip) on Mac for 
> development purposes.
> 
> The issues with excel are two-fold: XLSX files get unzipped automatically and 
> a useless XML file remains, while uploading an XLS file results in: "The 
> uploaded binary file contains inappropriate content". I've tried adding
> 
> <datatype extension="xls" type="galaxy.datatypes.binary:Binary" 
> display_in_upload="true"/>
> <datatype extension="xlsx" type="galaxy.datatypes.binary:Binary" 
> display_in_upload="true"/>
> 
> to datatypes_conf.xml and selecting XLS and XLSX as datatype during upload 
> but to no avail (the errors don't change).
> 
> A temporary workaround we thought of was to first zip the files before 
> uploading, that way Galaxy would unzip them and we'd be left with the raw 
> excel files. At first this seemed to work but the conversion did not. 
> Furthermore, downloading the files and trying to open them failed. A quick 
> 'diff' between the original and mangled files show differences practically 
> throughout the whole file!
> 
> Now, my questions are as follows. Has work been underway to support excel 
> natively? Is there a way to have Galaxy simply accept uploaded files without 
> any interpretation? What happens inside Galaxy that corrupts the excel files 
> during unpacking?
> 
> Thank you very much and I apologize if I somehow missed something obvious or 
> if these questions have been asked before.
> 
> Kind regards,
> Siemen Sikkema
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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