Many common bioinformatics applications are available on the Tool Shed already and so a common development task is to integrate scripts of various complexity into Galaxy.
Consider the following small Perl script.
.. literalinclude:: writing/gc_content.pl :language: perl
One can build a tool for this script as follows and place the script in
the same directory as the tool XML file itself. The special value
$__tool_directory__ here refers to the directory your tool lives in.
.. literalinclude:: writing/gc_content.xml :language: xml