--- a/msconvert3.xml	Thu Jun 20 16:08:23 2013 -0400
+++ b/msconvert3.xml	Fri Jul 12 12:45:51 2013 -0400
@@ -116,7 +116,7 @@
 
     <!-- BEGIN_VERSION_DEFAULT -->
     <conditional name="type">
-      <param name="input_type" type="select" label="Input Type">
+      <param name="input_type" type="select" label="Input Type" help="select file type of input data from history- mzml, mzXML, mgf or ms2. then select appropriate input file from drop down menu depending on input in history">
         <option value="mzml">mzML</option>
         <option value="mzxml">mzXML</option>
         <option value="mgf">mgf</option>
@@ -136,7 +136,7 @@
       </when>
     </conditional>
     <!-- END_VERSION_DEFAULT -->    
-    <param name="output_type" type="select" label="Output Type">
+    <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is The standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details).">
       <option value="mzML">mzML (indexed)</option>
       <option value="unindexed_mzML">mzML (unindexed)</option>
       <option value="mzXML">mzXML (indexed)</option>      
@@ -145,7 +145,7 @@
       <option value="ms2">ms2</option>  
     </param>    
     <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
+      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (see also peaklist processing)" />
       <when value="false" />
       <when value="true">
         <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
@@ -363,7 +363,7 @@
   <help>
 **What it does**
 
-Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
+Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
 
 You can view the original documentation here_.
     

--- a/msconvert3_raw.xml	Thu Jun 20 16:08:23 2013 -0400
+++ b/msconvert3_raw.xml	Fri Jul 12 12:45:51 2013 -0400
@@ -114,10 +114,10 @@
 
   <inputs>
     <!-- BEGIN_VERSION_RAW -->
-    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
+    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/>
     <!-- END_VERSION_RAW -->
 
-    <param name="output_type" type="select" label="Output Type">
+    <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is the standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)">
       <option value="mzML">mzML (indexed)</option>
       <option value="unindexed_mzML">mzML (unindexed)</option>
       <option value="mzXML">mzXML (indexed)</option>      
@@ -126,7 +126,7 @@
       <option value="ms2">ms2</option>  
     </param>    
     <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
+      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (also called as peaklist processing)" />
       <when value="false" />
       <when value="true">
         <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
@@ -353,6 +353,21 @@
     
 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
 
+**Recommended**
+
+For X!tandem searches: Use mzml format generated from RAW file.
+
+                                       RAW → mzml
+
+For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter.
+
+                                       RAW → mzml → MGF (ProteinPilot)
+
+For MaxQuant searches: Use RAW file as an input.
+
+For OMSSA : Use MGF format generated from mzml file using MGF formatter.
+
+                                       RAW → mzml → MGF (Mascot)
 ------
 
 **Citation**