There are a few tools that do this type of analysis. Search at the top of the tool panel with the keyword "pca" and each will come up. Review the tools forms to find the one that fits your data/goals.
Thanks, Jen, Galaxy team
This answer only applies to RNA-Seq analysis
The DESeq2 wrapper of IUC has a few built-in plots. If I'm not mistaken the MDS or PCA are also included. They only need count-tables from your RNA-Seq experiment as input and the rest is done automatically (estimating log fold changes and using those for MDS, not the read counts). You have to estimate the expression levels in your BAM files first (currently by using htseq-count, featureCounts will be available within a short time too)