--- a/Protein_report_processing.xml	Tue Aug 23 19:26:29 2016 -0400
+++ b/Protein_report_processing.xml	Tue Aug 23 20:03:58 2016 -0400
@@ -14,8 +14,8 @@
     <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
   </requirements>
   <inputs>
-    <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output" multiple="true"/>
-    <param type="select" name="use_metric" label="Select Report File Value for Qunatification">
+    <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
+    <param type="select" name="use_metric" label="Select Report File Value for Quantification">
       <option value="Validated_Peptides">#Validated Peptides</option>
       <option value="Peptides">#Peptides</option>
       <option value="Unique">#Unique</option> 
@@ -68,5 +68,85 @@
     </test>
   </tests>
   <help>
+Pre-Processing
+^^^^^^^^^^^^^^
+
+This tool will read in a Peptideshaker *Report* file (tab-delimited
+txt file) and process them to generate
+a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
+
+--------------
+
+  **Note:** The baits in the baitfile for this version need to be in
+  the same order as the files selected.
+
+
+**1) Peptideshaker File Inputs**
+
+Select the corresponding *Report* here.
+
+
+**2) Select Report File Value for Quantification**
+
+Select the column that should be used in calculating SAINT scores.
+
+**3) Create Prey File**
+
+Select whether or not you would like APOSTL to generate a prey file.
+
+When making a prey file, APOSTL queries a user provided FASTA database
+(see below) in order to extract protein amino acid lengths and gene
+names. This may take several minutes depending on your computer and if
+your Galaxy distribution is cluster enabled. Some users may want to run
+SAINTexpress using the same data set while changing which baits are
+considered test or control. It is useful to toggle **Create Prey File**
+off in order to save time by circumventing this step as the same prey
+file can be used for both SAINTexpress runs.
+
+**4) Provide Uniprot FASTA database**
+
+Please specify a FASTA file containing the protein sequence. You can
+download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
+http://www.uniprot.org/downloads. For computing efficiency,
+please limit your FASTA file to your species of interest. It is
+generally advised to use the same FASTA database that was used for your
+database searches during peptide and protein ID.
+
+**5) Are You Providing Your Own Bait File?**
+
+Users have two options for providing a *Bait* file. If you would like to
+create your own *Bait* file, select Yes and designate the file below. If
+you would like to use the **Bait Create** tool to create a *Bait* file
+within Galaxy, please select No and proceed to the **Bait Create** tool.
+
+**6) Bait File**
+
+If you selected Yes above, please specify the *Bait* file you would like
+to provide. If you selected No above, ignore this argument and proceed
+to the **Bait Create** tool.
+
+    **Note:** Individual bait names must match to the sample names
+    within your Scaffold or MaxQuant output exactly and must contain no
+    whitespace characters (e.g. spaces) or dashes.
+
+**7) Bait Create**
+
+Using the **Bait Create** tool, you can create your *bait.txt* file.
+
+    **Note:** Individual bait names must match to the sample names
+    within your Scaffold or MaxQuant output exactly and must contain no
+    whitespace characters (e.g. spaces) or dashes.
+
+APOSTL uses this bait file to find the user's baits of interest within a
+*Samples Report* or *peptides.txt* file and when preparing the
+*inter.txt* file.
+
+--------------
+
+Once your parameters have been finalized, please press the Execute
+button to start processing. This may take a few minutes. Once your
+process has been completed, you will see your *Bait File, Prey File,*
+and *Inter File* on the right hand side of your panel highlighted in
+green.
   </help>
 </tool>