Mercurial > repos > miller-lab > genome_diversity

diff average_fst.xml @ 22:95a05c1ef5d5

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update to devshed revision aaece207bd01
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 11 Mar 2013 11:28:06 -0400
parents d6b961721037
children 248b06e86022
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--- a/average_fst.xml	Mon Nov 05 12:44:17 2012 -0500
+++ b/average_fst.xml	Mon Mar 11 11:28:06 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="gd_average_fst" name="Overall FST" version="1.1.0">
+<tool id="gd_average_fst" name="Overall FST" version="1.2.0">
   <description>: Estimate the relative fixation index between two populations</description>
 
   <command interpreter="python">
@@ -21,8 +21,8 @@
 
     <conditional name="data_source">
       <param name="ds_choice" type="select" format="integer" label="Frequency metric">
-          <option value="0" selected="true">sequence coverage</option>
-          <option value="1">estimated genotype</option>
+          <option value="0">sequence coverage</option>
+          <option value="1" selected="true">estimated genotype</option>
       </param>
       <when value="0">
         <param name="min_value" type="integer" min="1" value="1" label="Minimum total read count for a population" />
@@ -95,10 +95,10 @@
 
 The program prints the following measures of FST for the two populations.
 
-1. The formulation by Sewall Wright (average over FSTs for all SNPs).
-2. The Weir-Cockerham estimator (average over FSTs for all SNPs).
-3. The Reich-Patterson estimator (average over FSTs for all SNPs).
-4. The population-based Reich-Patterson estimator.
+1. The Reich-Patterson estimator (average over FSTs for all SNPs).
+2. The population-based Reich-Patterson estimator.
+3. The formulation by Sewall Wright (average over FSTs for all SNPs).
+4. The Weir-Cockerham estimator (average over FSTs for all SNPs).
 
 If randomizations were requested, it prints a summary for each of the four definitions of FST that includes the maximum and average value, and the highest-scoring population pair (if any scored higher than the two user-specified populations).
 
@@ -123,10 +123,10 @@
 - output::
 
    Using 37847 SNPs, we compute:
+   Average Reich-Patterson FST is 0.31012.
+   The population-based Reich-Patterson Fst is 0.33625.
    Average Wright FST is 0.22810.
    Average Weir-Cockerham FST is 0.30813.
-   Average Reich-Patterson FST is 0.31012.
-   The population-based Reich-Patterson Fst is 0.33625.
 
   </help>
 </tool>