--- a/extract_flanking_dna.xml	Tue Oct 23 14:38:04 2012 -0400
+++ b/extract_flanking_dna.xml	Mon Nov 05 12:44:17 2012 -0500
@@ -12,13 +12,13 @@
   </command>
 
   <inputs>
-    <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
-    <param name="output_format" type="select" format="integer" label="output format">
+    <param format="tabular" name="input" type="data" label="SNP dataset"/>
+    <param name="output_format" type="select" format="integer" label="Output format">
         <option value="fasta" selected="true">FastA format</option>
-        <option value="primer3">Primer3 input</option>
+        <option value="primer3">Boulder-IO (for Primer3)</option>
     </param>
     <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>
@@ -53,17 +53,31 @@
 
   <help>
 
+**Dataset formats**
+
+The input dataset is in tabular_ format and must contain a scaffold or 
+chromosome column and a position column.  The output is in fasta_ format or
+Boulder-IO_ format used by Primer3.
+(`Dataset missing?`_)
+
+.. _tabular: ./static/formatHelp.html#tab
+.. _fasta: ./static/formatHelp.html#fasta
+.. _Boulder-IO: ./static/formatHelp.html#boulder
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
 **What it does**
 
-  This tool reports a DNA segment containing each SNP, with up to 200 nucleotides on
-  either side of the SNP position, which is indicated by "n". Fewer nucleotides
-  are reported if the SNP is near an end of the assembled genome fragment.
+This tool reports a DNA segment containing each SNP, with up to 200 nucleotides 
+on either side of the SNP position, which is indicated by "n". Fewer nucleotides
+are reported if the SNP is near an end of the assembled genome fragment.
 
 -----
 
 **Example**
 
-- input file::
+- input (gd_snp format)::
 
     chr2_75111355_75112576    314  A  C  L  F  chr2   75111676  C  F  15  4  53   2   9  48   Y  96   0.369  0.355  0.396  0
     chr8_93901796_93905612   2471  A  C  A  A  chr8   93904264  A  A  8   0  51   10  2  14   Y  961  0.016  0.534  0.114  2
@@ -77,7 +91,7 @@
     chr19_39866997_39874915  3117  C  T  P  P  chr19  39870110  C  P  3   7  65   14  2  32   Y  6    0.321  0.911  0.462  4
     etc.
 
-- output file::
+- output (FastA format)::
 
     > chr2_75111355_75112576 314 A C
     TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT