I am currently adapting version 0.11.2 of FastQC as a Galaxy tool, as we want to include it in our workflow. As currently only an older version of the tool is available on the Galaxy Toolshed we thought of making it public. Unfortunately writing (output file comparison) tests for the new version has proven difficult as it generates HTML output in a single line of text (no newline characters included in the ascii text document of ~300 KB). While it might be possible to include regular expressions for date and time stamps in the output, it seems difficult to provide a good test under this circumstance.
A possibility would be to include the .txt output of FastQC and compare that one to a sample. Does anyone with more experience in Galaxy testing have more suggestions?