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The GUI comes with the Schloss SOP already set for you to use. You can load a pipeline by clicking on the name. You can run the SOP with Pat's example files or go through the commands inserting your own files.
The Analysis pipeline includes the collect.single, rarefaction.single, catchall, summary.single, heatmap.bin, heatmap.sim, venn, summary.shared, tree.shared, parsimony, unifrac.weighted, unifrac.unweighted, dist.shared, pcoa, nmds, amova, corr.axes, metastats and phylo.diversity.