# HG changeset patch
# User iuc
# Date 1479147074 18000
# Node ID 6f7ff8a3bd792ff94332d18fb0cc3d880bd7246c
# Parent  b0d6eb76ad87a8e497ad97afe1915577400f1cbf
planemo upload for repository https://github.com/stamatak/standard-RAxML commit bcfc8451fa622a6bf3aa31fa1e308c394feefb38

diff -r b0d6eb76ad87 -r 6f7ff8a3bd79 raxml.py
--- a/raxml.py	Sat Jun 25 19:34:35 2016 -0400
+++ b/raxml.py	Mon Nov 14 13:11:14 2016 -0500
@@ -366,5 +366,6 @@
     infof.write(options.__repr__())
     infof.write('\nOM: CLI options DEBUG END\n')
 
+
 if __name__ == "__main__":
     __main__()
diff -r b0d6eb76ad87 -r 6f7ff8a3bd79 raxml.xml
--- a/raxml.xml	Sat Jun 25 19:34:35 2016 -0400
+++ b/raxml.xml	Mon Nov 14 13:11:14 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
+<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2">
     <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
     <requirements>
         <requirement type='package' version="8.2.4">raxml</requirement>
@@ -178,7 +178,7 @@
                 <param name="base_model" type="select" label="Substitution Model" help="--base-model">
                     <option value="GTRCAT">GTRCAT</option> 
                     <option value="GTRCATI">GTRCATI</option> 
-                    <option value="GTRGAMMA" select="true">GTRGAMMA</option>
+                    <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
                     <option value="GTRGAMMAI">GTRGAMMAI</option>
                 </param>
             </when>
@@ -186,13 +186,13 @@
                 <param name="aa_model_empirical_base_frequencies"
                     type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
                 <param name="base_model" type="select" label="Substitution Model (--base_model)">
-                    <option value="PROTCAT" select="true">PROTCAT</option>
+                    <option value="PROTCAT" selected="true">PROTCAT</option>
                     <option value="PROTCATI">PROTCATI</option>
                     <option value="PROTGAMMA">PROTGAMMA</option>
                     <option value="PROTGAMMAI">PROTGAMMAI</option>
                 </param>
                 <param name="aa_search_matrix" type="select" label="Matrix" help="(--aa_search_matrix)">
-                    <option value="DAYHOFF" select="true">DAYHOFF</option>
+                    <option value="DAYHOFF" selected="true">DAYHOFF</option>
                     <option value="DCMUT">DCMUT</option>
                     <option value="JTT">JTT</option>
                     <option value="MTREV">MTREV</option>