--- a/extract_primers.xml	Tue Oct 23 14:38:04 2012 -0400
+++ b/extract_primers.xml	Mon Nov 05 12:44:17 2012 -0500
@@ -11,9 +11,9 @@
   </command>
 
   <inputs>
-    <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
+    <param format="tabular" name="input" type="data" label="SNP dataset"/>
     <conditional name="override_metadata">
-      <param name="choice" type="select" format="integer" label="choose columns">
+      <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the columns in the metadata, all others need the columns chosen." >
         <option value="0" selected="true">No, get columns from metadata</option>
         <option value="1" >Yes, choose columns</option>
       </param>
@@ -46,30 +46,46 @@
 
   <help>
 
+**Dataset formats**
+
+The input dataset is in tabular_ format and must contain a scaffold or 
+chromosome column and a position column.  The output dataset is in text_ 
+format as described below.
+(`Dataset missing?`_)
+
+.. _tabular: ./static/formatHelp.html#tab
+.. _text: ./static/formatHelp.html#text
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
 **What it does**
 
-  This tool extracts primers for SNPs in the dataset using the Primer3 program.
-  The first line of output for a given SNP reports the name of the assembled
-  contig, the SNP's position in the contig, the two variant nucleotides, and
-  Primer3's "pair penalty".  The next line, if not blank, names restriction
-  enzymes (from the user-adjustable list) that differentially cut at that
-  site, but do not cut at any other position between and including the
-  primer positions.  The next lines show the SNP's flanking regions, with
-  the SNP position indicated by "n", including the primer positions and an
-  additional 3 nucleotides.
+This tool extracts primers for SNPs in the dataset using the Primer3 program
+(Steve Rozen and Helen J. Skaletsky, 2000).
+The first line of output for a given SNP reports the name of the assembled
+contig, the SNP's position in the contig, the two variant nucleotides, and
+Primer3's "pair penalty".  The next line, if not blank, names restriction
+enzymes (from the user-adjustable list) that differentially cut at that
+site, but do not cut at any other position between and including the
+primer positions.  The next lines show the SNP's flanking regions, with
+the SNP position indicated by "n", including the primer positions and an
+additional 3 nucleotides.
+<!-- is this precomputed?? how, where is the user-adjustable list? -->
 
 -----
 
 **Example**
 
-- input file::
+- input (gd_snp format)::
 
     chr5_30800874_30802049    734   G  A  chr5   30801606   A  24  0  99   4  11  97   Y  496  0.502  0.033  0.215  6
     chr8_55117827_55119487    994   A  G  chr8   55118815   G  25  0  102  4  11  96   Y  22   0.502  0.025  2.365  1
     chr9_100484836_100485311  355   C  T  chr9   100485200  T  27  0  108  6  17  100  Y  190  0.512  0.880  2.733  4
     chr12_3635530_3637738     2101  T  C  chr12  3637630    T  25  0  102  4  13  93   Y  169  0.554  0.024  0.366  4
+    etc.
 
-- output file::
+- output::
 
     chr5_30800874_30802049 734 G A 0.352964
      BglII,MboI,Sau3AI,Tru9I,XhoII