--- a/APOSTL_Static_Bubblegraph_Generator.xml	Wed May 11 11:41:18 2016 -0400
+++ b/APOSTL_Static_Bubblegraph_Generator.xml	Wed May 11 12:51:14 2016 -0400
@@ -1435,5 +1435,99 @@
     </test>
   </tests>
   <help>
-  </help>
+Bubble Graph Generator
+^^^^^^^^^^^^^^^^^^^^^^
+
+This Bubble Graph Generator is static version of the APOSTL interactive affinity proteomics analysis 
+software developed to reformat affinity proteomics data (both spectral counting and MS1) for input 
+into the SAINTexpress statistical package and to visualize the output(s). APOSTL was developed at 
+H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL). 
+
+--------------
+
+**1) SAINT Output File**
+
+SAINTexpress generated *list.txt* file.
+
+    **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g.
+    "EGFR\_HUMAN" or "P00533").
+
+**2) Prey File**
+
+Please specify a *Prey* file for Bubble Graph creation. A *Prey* file
+should contain three columns: prey (protein) name, prey amino acid
+length, and prey gene name.
+
+**3) CRAPome File**
+
+Please specify an *CRAPome* file for Bubble Graph creation. An *Inter*
+file should contain five columns: IP name, Mapped Gene Symbol, Number of 
+Experiments (ratio), and Average spectral counts, and Max spectral counts.
+
+**4) Interactions File**
+
+Please specify an *Inter* file for Bubble Graph creation. An *Inter*
+file should contain four columns: IP name, bait name, prey name, and
+spectral counts or intensity values, depending on the mode of
+quantification.
+
+**5) X Axis Label**
+
+Selct the value to be used as the X axis in the Bubble Graph.
+
+**6) Y Axis Label**
+
+Selct the value to be used as the Y axis in the Bubble Graph.
+
+**7) Bubble Size**
+
+Selct the value to size the bubbles in the Bubble Graph. The "fixed"
+option will make all the bubbles the same size (must be used if no-crapome 
+file is provided).
+
+**8) Color**
+
+Crapome will color the bubbles acooring to their likelyhood of a good
+interaction. Fixed will make all the bubbles one color (must be used if no-crapome 
+file is provided).
+
+**9) SAINT Score Cutoff**
+
+SaintScore filter in range 0-1 (default 0.8)
+
+**10) Fold Change Cutoff**
+
+Fold Change filter in range -Inf to Inf (default 0)
+
+**11) NSAF Score Cutoff**
+
+NSAF Score filter in range -Inf to Inf (default 0)
+
+**12) Plot Theme**
+
+Select theme to be used when creating Bubble Graph.
+
+**13) Label Type**
+
+Select the type of labeling, no labels, lable those greater than cutoff, and 
+all bubbles labeled.
+
+**14) Label Color**
+
+Select label color.
+
+**15) Bubble Color**
+
+Select color of Bubble interior. If *8* is set to crapome this will act as the good 
+crapome score. If *8* is set to fixed this will be the bubble color.
+
+**16) Outline Color**
+
+Select the bubble outline color.
+
+**17) Crapome Filter Color**
+
+Select color of crapome filtering. If *8* is set to crapome this will act as the poor 
+crapome score. If *8* is set to fixed this will not be used.
+
 </tool>