# HG changeset patch
# User rdvelazquez
# Date 1542734312 18000
# Node ID e445c2dc2cce7bc722ca085fd4c0c7d301065834
# Parent  f2ee2e0bde56852caa1e2bafa01fae6bdb4792b2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty

diff -r f2ee2e0bde56 -r e445c2dc2cce hyphy_fade.xml
--- a/hyphy_fade.xml	Tue Nov 20 10:16:35 2018 -0500
+++ b/hyphy_fade.xml	Tue Nov 20 12:18:32 2018 -0500
@@ -9,21 +9,33 @@
   <version_command>HYPHYMP --version | tail -n 1 | awk '{print
   $1}'</version_command>
   <command detect_errors="exit_code"><![CDATA[
-    ln -s '$input_file' fade_input.fa &&
-    ln -s '$input_nhx' fade_input.nhx &&
-    echo `pwd`/fade_input.fa >> tool_params &&
-    echo `pwd`/fade_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    echo '$grid_points' >> tool_params &&
-    echo '$substitutionmodel' >> tool_params &&
-    echo '$posteriorEstimationMethod' >> tool_params &&
-    echo '$mcmc' >> tool_params &&
-    echo '$chain_length' >> tool_params &&
-    echo '$samples' >> tool_params &&
-    echo '$samples_per_chain' >> tool_params &&
-    echo '$concentration' >> tool_params &&
-    echo '$branches' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
+    #if $posteriorEstimationMethod == 3:
+      ln -s '$input_file' fade_input.fa &&
+      ln -s '$input_nhx' fade_input.nhx &&
+      echo `pwd`/fade_input.fa >> tool_params &&
+      echo `pwd`/fade_input.nhx >> tool_params &&
+      echo '$branches' >> tool_params &&
+      echo '$grid_points' >> tool_params &&
+      echo '$substitutionmodel' >> tool_params &&
+      echo '$posteriorEstimationMethod' >> tool_params &&
+      echo '$concentration' >> tool_params &&
+      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
+    #else:
+      ln -s '$input_file' fade_input.fa &&
+      ln -s '$input_nhx' fade_input.nhx &&
+      echo `pwd`/fade_input.fa >> tool_params &&
+      echo `pwd`/fade_input.nhx >> tool_params &&
+      echo '$branches' >> tool_params &&
+      echo '$grid_points' >> tool_params &&
+      echo '$substitutionmodel' >> tool_params &&
+      echo '$posteriorEstimationMethod' >> tool_params &&
+      echo '$mcmc' >> tool_params &&
+      echo '$chain_length' >> tool_params &&
+      echo '$samples' >> tool_params &&
+      echo '$samples_per_chain' >> tool_params &&
+      echo '$concentration' >> tool_params &&
+      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
+    #end if
     ]]></command>
   <inputs>
     <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>