diff raxml.xml @ 22:ec5e58cd3a68 draft

planemo upload commit db9228a4b4042ad9493237882a8266529bb69931

--- a/raxml.xml	Tue Nov 03 16:06:50 2015 -0500
+++ b/raxml.xml	Tue Nov 03 16:12:34 2015 -0500
@@ -134,9 +134,7 @@
     #end if
     ## (-T) see elsewhere
     ## (-u)
-    #if str ($selExtraOpts.use_median_approximation) == "true":
-        --use_median_approximation
-    #end if
+    $selExtraOpts.use_median_approximation
     ## (-U)
     $selExtraOpts.save_memory_gappy_alignments
     ## (-V)
@@ -383,7 +381,7 @@
             ## (-t)
             <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" help="Specify a user starting tree file name in Newick format." />
             ## (-T) is hard-coded in the required options section
-            <param name="use_median_approximation" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
+            <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
             ## (-U)
             <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" />
             ## (-V)