# HG changeset patch
# User bornea
# Date 1460989992 14400
# Node ID 67631a6405345667f2fdf027fecd3d0865bb4ec7
# Parent  3243333b2f39cc36fcb33ce7fea6911e508327b1
Uploaded

diff -r 3243333b2f39 -r 67631a640534 saint_wrapper.xml
--- a/saint_wrapper.xml	Tue Mar 15 16:25:14 2016 -0400
+++ b/saint_wrapper.xml	Mon Apr 18 10:33:12 2016 -0400
@@ -39,23 +39,63 @@
     </test>
   </tests>
   <help>
-**Running SAINT Express**
+SAINTexpress
+------------
+
+This tool will read in a *Bait File, Prey File,* and *Inter File* and
+analyze them using the latest version of SAINTexpress.
 
-INPUTS:
+**1) Interactions File**
+
+Please specify an *Inter* file for SAINTexpress analysis. 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.
 
-Interactions File: Should contain four columns: IP name, bait name, prey name, and spectral counts or intensity values, depending on the mode of quantitation.
+**2) Prey File**
+
+Please specify a *Prey* file for SAINTexpress analysis. A *Prey* file
+should contain three columns: prey (protein) name, prey amino acid
+length, and prey gene name.
 
-Prey File: Should contain three columns: prey (protein) name, prey protein length, and prey gene name.  
+**3) Bait File**
+
+Please specify a *Bait* file for SAINTexpress analysis. A *Bait* file
+should have three columns: IP name, bait name, and the indicator for
+test and negative control purifications.
+
+**4) Number of Replicates**
 
-Bait File: Should have three columns: IP name, bait name, and the indicator for test and negative control purifications.
+The number of replicates (with largest spectral counts or intensities)
+to be used for probability calculation in each bait. This option is
+useful when some baits have more replicates than others.
+
+**5) Using Virtual Control Purifications by Compression**
 
-Number of Replicates: Sets the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait.  This option is useful when some baits have more replicates than others.
+Sets the number of virtual control purifications by compression. For
+instance, if you wish to take 4 largest spectral counts for controls,
+set **Number of Vitual Controls** to 4 and this variable to Yes.
+
+**6) Number of Virtual Controls**
+
+Specify the number of virtual control purifications by compression.
 
-Using Virtual Control Purification by Compression: Sets the number of virtual control purifications by compression.  For instance, if the user wishes to take 4 largest spectral counts for controls, set Number of Vitual Controls to 4 and this variable to yes.
+**7) Incorporate External Data Sources**
 
-Incorporate External Data Sources: To incorporate external data sources for computing the topology-aware probability score (TopoAvgP), the user must also provide the interaction database file that contains two columns: interaction identifier column and interaction/grouping information column. The first column is just for formality and thus can be filled in with anything (no white space) and it will not be utilized in the scoring. The second column must be formatted as a string of prey identifiers (consistent with the first column of the prey file) separated by a white space.
+To incorporate external data sources for computing the Topology-Aware
+Probability Score (TopoAvgP), the user must also provide the interaction
+database file that contains two columns: interaction identifier column
+and interaction/grouping information column. The first column is just
+for formality and thus can be filled in with anything (no white space)
+and it will not be utilized in the scoring. The second column must be
+formatted as a list of prey identifiers (consistent with the first
+column of the prey file) separated by a white space.
 
-------
+**8) External Data File**
+
+Specify external data file
+
+--------
 
 **Please cite**