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:
raw.data <- read.xlsx(commandArgs(trailingOnly=TRUE)),
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:
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) shows that Galaxy provided a filename
extension of ".dat".
I tried a workaround using this:
file=paste(commandArgs(trailingOnly=TRUE)), ".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" 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:
so the relevant entries in datatypes_conf.xml are:
<datatype extension="xls" type="galaxy.datatypes.binary.Xls"
<datatype extension="xlsx" type="galaxy.datatypes.binary.Xlsx"
and the relevant additions to binary.py are:
'''Class describing an Excel 2003 (xls) file'''
'''Class describing an Excel 2007 (xlsx) file'''
Any suggestions appreciated.
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