It would be nice if there was an easier way to set the analysis config of the clustalw component (i.e. in a comparative load where you are aligning the results of a jaccard or jocs run). A dropdown would probably not work as you might have run the jaccard or jocs in a previous pipeline and are just now doing the alignments.
One issue is that when this parameter is not set properly one has to remember to clear all the temp and output areas before rerunning or you will get duplicates in your output list that won't be discovered till load time.
Perhaps a check of file presence before creating the iterator would be helpful. This would allow you to change the component xml in the event you spell the parameter wrong.
Also it might be useful to have the analysis config file paths for the previously configured components somewhere on the page to allow for cutting and pasting.