Assuming everything is generated correctly for the html report, what you're 
probably running into is Galaxy's html sanitization.  In your Galaxy instance's 
universe_wsgi.ini you can set the following option (to false) to disable this:

# Sanitize All HTML
# By default, all tool output served as 'text/html' will be sanitized
# thoroughly. This can be disabled if you have special tools that require
# unaltered output.
#sanitize_all_html = True

-Dannon

On Mar 22, 2012, at 7:35 PM, Jose Navas wrote:

> Hi Galaxy developers,
> 
> I have a tool that generates an html output which executes some javascript 
> functions that are defined in a *.js file. I put this file under the 
> $output1.files_path but when I display the html file in the galaxy browser, 
> it doesn't executes the Javascript. What can I do to execute Javascripts in 
> the Galaxy browser?
> 
> Thanks,
> 
> Jose
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