I have a problem with a tool wrapper I wrote handling input files with spaces 
in their names. If a user uploads a dataset that has spaces in the file name, 
e.g. "foo bar.xml"  file then even though my tool, which uses the last "tmp 
directory" method of handling multiple output files is provided by galaxy with 
a normal input filename like 
"/galaxy/production/database/files/006/dataset_6667.dat" the galaxy renames the 
output files to names based on the metadata like "foo bar.log" and "foo 
bar.nxs" output files, which don't get copied into the history.  I wonder if 
anyone ran into this issue before and how it was handled.


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