These are out-dated - there are a lot more parameters in 0.9.4. 

```
-i otu table: QIIME-formatted OTU table (first line is a comment line starting with '#', second line starts with '#OTU ID' followed by sample names). You must supply either this or the taxon table via '-t'.
-t taxon table: output from QIIME script summarize_taxa.py. You must supply either this or the otu table via '-i'.
-m mapfile: mapping file with an 'Env' column giving the source environments, and a 'SourceSink' column giving 'source' for source samples and 'sink' for sink samples.
-n number of restarts of Gibbs sampling (default 10)
-b number of burn-in iterations for Gibbs sampling (default 100)
-r rarefaction depth, 0 for none (default 1000)
--train_rarefaction training data rarefaction depth, 0 for none (default 1000)
-f sampleid_file, file containing list of samples to predict. Useful for parallel processing (default None).
-o outdir: output directory; default is '.'
-s predict source samples using leave-one-out predictions (default: FALSE)
--alpha1 alpha1: Dirichlet hyperparameter for taxa/genes in known environments (default: 1e-3)
--alpha2 alpha2: Dirichlet hyperparameter for taxa/genes in unknown environments (default: 1e-1)
--beta beta: Dirichlet hyperparameter for mixture of environments (default: 1e-2)
-R results file from previous run. If given, no predictions are made, only plotting and output files)
--tune_alphas: tune_ntrials Tune alpha values using cross-validation on the training set with this many trials (suggest at least 25); (default: 0, no tuning)
--color_ix: comma-separated list of color indices for alphabetical source environments
--eval_fit: fit_ntrials Evaluate quality of fit to the data using simulations. Ignored if less than or equal to --tune_alpha ntrials (default: 0)
-v: verbose output (default FALSE)
```