I am trying to write a Galaxy tool that will output an Excel file. 

Currently the tool wrapper calls an R script, which uses the "xlsx" package to read and write to and from Excel files.

After being invoked by Galaxy, the script is able to successfully read an input Excel file:

    suppressPackageStartupMessages(library(xlsx, quietly=TRUE));
    raw.data <- read.xlsx(commandArgs(trailingOnly=TRUE)[1]), sheetName="input_records");
   
The script then does its work on the data just read in.  Then, when the work is done, I'd like to output the results to an Excel file.  Here's where I run into a problem.  I first tried to output the result like this:

    write.xlsx(processed.data, file=commandArgs(trailingOnly=TRUE)[2]);

but write.xlsx throws an error.  Looks like  ".xls" and ".xlsx" are the only legal file extensions for the write.xlsx() function.  Inspecting commandArgs(trailingOnly=TRUE)[2] shows that Galaxy provided a filename extension of ".dat". 

I tried a workaround using this:

    write.xlsx(processed.data, file=paste(commandArgs(trailingOnly=TRUE)[2]), ".xls", sep="");
   
The write.xlsx function no longer throws an error (since the file name supplied as a parameter has an acceptable file extension) but now Galaxy won't display the result in the History.  If I look in Galaxy's database I see two files there corresponding to my tool's output.  Supposing that Galaxy assigned the result the name "dataset_87", then looking in the Galaxy database I see:

    dataset_87.dat
    dataset_87.dat.xls
   
"dataset_87.dat" is empty but visible to Galaxy (and so displayed as an empty dataset in the History window). "dataset_87.dat.xls" has the results I want but isn't displayed by Galaxy in the History window.

There might be R libraries that can write xls or xlsx files without requiring a ".xls" or ".xlsx" file extension.  That's a path I'm willing to explore.  That said, is there a configuration option I can set that'll let me continue to use write.xlsx()?

I've been working from the suggestions made on this helpful thread:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007807.html

so the relevant entries in datatypes_conf.xml are:

    <datatype extension="xls" type="galaxy.datatypes.binary.Xls" display_in_upload="true" />
    <datatype extension="xlsx" type="galaxy.datatypes.binary.Xlsx" display_in_upload="true" />
   
and the relevant additions to binary.py are:

    class Xls(Binary):
        '''Class describing an Excel 2003 (xls) file'''

        file_ext='xls'
       
    class Xlsx(Binary):
        '''Class describing an Excel 2007 (xlsx) file'''

        file_ext='xlsx'       
   
Any suggestions appreciated.

Thanks, Patrick