galaxyproject/tools-devteam — pull request #17 by aerval (2014-10-23 21:04:16+00:00)
Title: Fastqc 0.11.2

This implements new version 0.11.2 of [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), including:

Changes
----

1. new package that downloads the new program version
2. necessary changes in the tool to support the new version including some code documentation, bug fixing etc.
3. Additional (optional) input: custom limits file that allows setting of custom warning thresholds and exclusion of submodules from the result
4. Additional output: Text file output, as it contains (most of) the raw data in the generated plots and is easier to use in additional analysis and data interpretation pipelines
5. Update of the integrated test and addition of one more. **Note**: as I mentioned [before](https://biostar.usegalaxy.org/p/9199/), the generated HTML file contains only a single line of code. I might be possible to still compare it in a test via regular expressions but would probably very tedious. I am not sure what the "official" way of handeling this would be but circumvent the problem with the additional text output file that contains essentially the same information as the HTML file. As it now compare that file too, I think the test should find almost all problems that could come up.

Suggestion
----
I might be nice to make each of the two output files optional

Credits
----
Devteam and IUC for the last version
T. McGowan for [first implementation of the new version](https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc)