For some of the recent tools we have developed on our Galaxy instance (
we were using the approach mentioned in the wiki for writing a single HTML
output file with links to additional output files (images, csv etc.,). This
is much nicer than generating multiple output files in the history panel.
However, the exported histories did not contain these included files. I
have now fixed this bug on our instance and have also created a pull
request on Github (#417 <https://github.com/galaxyproject/galaxy/pull/417>
1. Include the extra_files_path attribute on the dataset which is being
2. Check if there are any files in the extra_files_path for each dataset
that will be included in the archive.
3. If there are files present, create a new directory and save files to
this directory. This directory will then be included in exported archive.
The dataset's history ID is appended to both the directory and the
dataset's name to prevent conflict with a dataset of the same name.
A simple tool to test html export with included files is available at: