--- a/peptide_shaker.xml	Wed Jun 26 16:12:25 2013 -0400
+++ b/peptide_shaker.xml	Fri Jul 19 11:06:52 2013 -0400
@@ -88,15 +88,15 @@
     <exit_code range="1:" level="fatal" description="Job Failed" />
   </stdio>
   <inputs>
-    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
-    <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" />
-    <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units">
+    <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>
+    <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" />
+    <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
       <option value="1">Parts per million (ppm)</option>
       <option value="0">Daltons</option>
     </param>    
-    <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" />
-    <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" />
-    <param name="enzyme" type="select" label="Enzyme">
+    <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
+    <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" help="Provide error value for fragment ions, based on instrument used"/>
+    <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
       <option value="Trypsin">Trypsin</option>
       <option value="Arg-C">Arg-C</option>
       <option value="CNBr">CNBr</option>
@@ -123,33 +123,33 @@
       <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
       <option value="Semi-Glu-C">Semi-Glu-C</option>      
     </param>
-    <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" />
-    <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
+    <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/>
+    <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
       <options from_file="searchgui_mods.loc">
         <column name="name" index="0" />
         <column name="value" index="0" />
       </options>
     </param>
-    <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
+    <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
       <options from_file="searchgui_mods.loc">
         <column name="name" index="0" />
         <column name="value" index="0" />
       </options>
     </param>        
-    <param name="min_charge" label="Minimum Charge" value="2" type="integer" />
-    <param name="max_charge" label="Maximum Charge" value="4" type="integer" />
-    <param name="forward_ion" label="Forward Ion" type="select">
+    <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
+    <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
+    <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
       <option value="a">a</option>
       <option value="b" selected="true">b</option>
       <option value="c">c</option>
     </param>
-    <param name="reverse_ion" label="Reverse Ion" type="select">
+    <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
       <option value="x">x</option>
       <option value="y" selected="true">y</option>
       <option value="z">z</option>
     </param>
     <conditional name="advanced">
-      <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" />
+      <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/>
       <when value="false" />
       <when value="true">
         <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
@@ -166,7 +166,9 @@
       </when>
     </conditional>
     <conditional name="processing_options">
-      <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" />
+      <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" help="Select and provide False Discovery Rate (FDR) levels at the peptide, protein, and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM’s and A score options for post-translational modifications (PTM’s). See this link_ for more details
+
+ .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />
       <when value="false" />
       <when value="true">
         <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
@@ -184,7 +186,7 @@
       </when>
     </conditional>    
     <conditional name="filtering_options">
-      <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" />
+      <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"/>
       <when value="false" />
       <when value="true">
         <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
@@ -213,7 +215,7 @@
   <help>
 **What it does**
 
-Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the result via PeptideShaker.
+Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.
 
 ------