diff hyphy_sm19.xml @ 5:5f1830cb9135 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"

--- a/hyphy_sm19.xml	Mon Feb 17 14:53:22 2020 -0500
+++ b/hyphy_sm19.xml	Thu Feb 20 18:09:55 2020 -0500
@@ -63,15 +63,76 @@
         </test>
     </tests>
     <help><![CDATA[
-This analysis implements canonical and modified versions of the Slatkin-Maddison
-phylogeny based test for population segregation. The test estimates the minimum
-number of migration events using maximum parsimony, and then evaluating whether
-or not this number is lower than expected in a panmictic or unstructured
-population using permutation tests.
+
+SM2019 : Structured Slatkin-Maddison
+====================================
+    
+What does this do?
+------------------
+
+Test for evidence of genetically segregated populations, using a "detuned" version of 
+the Slatkin-Maddison test.
+
+Brief description
+-----------------
+
+This analysis implements canonical and modified versions of the
+Slatkin-Maddison phylogeny based test for population segregation. The
+test estimates the minimum number of migration events using maximum
+parsimony, and then evaluating whether or not this number is lower than
+expected in a panmictic or unstructured population using permutation
+tests
+
+Input
+-----
+
+1. A phylogenetic tree in the *Newick* format
+
+Note: assumes that leaf names that can be partitioned into sets using regular expressions
+
+For example
+
+::
+
+    ((((((((x_US_x_A_01C:0.0125396,(((((x_US_x_A_01P:0.00887628,((
+    x_US_x_A_08P:-0.000190918,x_US_x_A_11P:0.00313157):0.0106883,
+    x_US_x_A_14C:0.0103815):0.00311658):0.00120812,x_US_x_A_09P:0.00320468):
+    0.0108828,x_US_x_A_12P:0.00732672):0.00596663,x_US_x_A_07C:0.00449846):0
+    .00639319,((((x_US_x_A_02P:-2.62303e-05,x_US_x_A_05P:0.00591507):0.
+    000156788,x_US_x_A_04P:0.00576826):0.00907366,((x_US_x_A_03P:0.00941548,
+    x_US_x_A_14P:0.00866127):0.00229499,x_US_x_A_13P:0.0209192):0.00469629):
+    0.0146758,(x_US_x_A_10P:0.000156443,x_US_x_A_15P:0.00578946):0.00472532)
+    :0.0103079):0.00733948):0.00228489,x_US_x_A_06P:0.00557974):0.00472981,
+    x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905,
+    x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e-
+    06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538,
+    x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4.
+    34574e-06,x_US_x_A_15C:-4.34574e-06);
+    
+Which can be partitioned into two groups of leaves, those that end in "P", and those that 
+end in "C"
+
+1. Reg-exp 1: `P^`
+2. Reg-exp 2: `C^`
+
+
+Output
+------
+
+A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
+
+A custom visualization module for viewing these results is available (see http://vision.hyphy.org/Slatkin for an example)
+
+Further reading
+---------------
+
+https://github.com/veg/hyphy-analyses/tree/master/SlatkinMaddison
+
+
     ]]></help>
     <expand macro="citations">
         <citation type="bibtex">
-            @UNPUBLISHED{slatkin,
+            @PUBLISHED{slatkin,
                 author = "Slatkin M, Maddison WP",
                 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
                 year = "1989",