diff select_snps.xml @ 21:d6b961721037

Miller Lab Devshed version 4c04e35b18f6

--- a/select_snps.xml	Tue Oct 23 14:38:04 2012 -0400
+++ b/select_snps.xml	Mon Nov 05 12:44:17 2012 -0500
@@ -11,12 +11,12 @@
   </command>
 
   <inputs>
-    <param format="tabular" name="input" type="data" label="Selected SNPS dataset">
+    <param format="tabular" name="input" type="data" label="SNP dataset">
       <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
     </param>
     <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
     <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 column information in the metadata, all others must be chosen." >
         <option value="0" selected="true">No, get columns from metadata</option>
         <option value="1" >Yes, choose columns</option>
       </param>
@@ -50,17 +50,27 @@
 
   <help>
 
+**Dataset formats**
+
+The input and output datasets are in tabular_ format.
+(`Dataset missing?`_)
+
+.. _tabular: ./static/formatHelp.html#tab
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
 **What it does**
 
-  This tool attempts to select a specified number of SNPs from the dataset, making them
-  approximately uniformly spaced relative to the reference genome. The number
-  actually selected may be slightly more than the specified number.
+This tool attempts to select a specified number of SNPs from the dataset, making
+them approximately uniformly spaced relative to the reference genome. The number
+actually selected may be slightly more than the specified number.
 
 -----
 
 **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
@@ -74,7 +84,7 @@
     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::
 
     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