--- a/multigps.xml	Wed Dec 14 11:30:21 2016 -0500
+++ b/multigps.xml	Wed Dec 14 11:31:49 2016 -0500
@@ -445,6 +445,7 @@
 **Options**
 
 * **Loading data:**
+
  - **Optional file containing file containing reads from a control experiment** - must be same format as input experiment
  - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
  - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
@@ -453,6 +454,7 @@
  - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).
 
 * **Scaling control vs signal counts:**
+
  - **Use signal vs control scaling?** - Flag to turn off auto estimation of signal vs control scaling factor
  - **Use the median signal/control ratio as the scaling factor?** - Flag to use scaling by median ratio (default = scaling by NCIS).
  - **Use scaling by regression on binned tag counts?** - Flag to use scaling by regression (default = scaling by NCIS).
@@ -462,6 +464,7 @@
  - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.
 
 * **Running MultiGPS:**
+
  - **binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
  - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
  - **Perform binding model updates?** - Perform binding model updates?
@@ -478,6 +481,7 @@
  - **Optional file containing a set of regions to ignore during MultiGPS training** - File containing a set of regions to ignore during MultiGPS training. It’s a good idea to exclude the mitochondrial genome and other ‘blacklisted’ regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments. MultiGPS will waste time trying to model binding events in these regions, even though they will not typically appear significantly enriched over the control (and thus will not be reported to the user).
 
 * **MultiGPS priors:**
+
  - **Perform inter-experiment positional prior?** - Flag to turn off inter-experiment positional prior (default=on).
  - **Probability that events are shared across conditions** - Probability that events are shared across conditions.
  - **Perform both motif-finding and motif priors?** - Flag to turn off motif-finding and motif priors.
@@ -487,11 +491,13 @@
  - **Maximum motif width for MEME** - maxw arg for MEME.
 
 * **Reporting binding events:**
+
  - **Minimum Q-value (corrected p-value) of reported binding events** - Minimum Q-value (corrected p-value) of reported binding events.
  - **Minimum event fold-change vs scaled control** - Minimum event fold-change vs scaled control.
  - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests.
  - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
  - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
+
     </help>
     <expand macro="citations" />
 </tool>