# HG changeset patch
# User rdvelazquez
# Date 1546965284 18000
# Node ID f078fc88982d173758c0752fab2ff837ae0cf4c7
# Parent  a046be57e024d2cd63f4ed3dd43a5508d18e1b93
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty

diff -r a046be57e024 -r f078fc88982d hyphy_relax.xml
--- a/hyphy_relax.xml	Tue Jan 08 10:58:10 2019 -0500
+++ b/hyphy_relax.xml	Tue Jan 08 11:34:44 2019 -0500
@@ -8,15 +8,15 @@
     <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-    #if $treeAnnotations == 1:
+    #if $treeAnnotations == 2:
         ln -s '$input_file' relax_input.fa &&
         ln -s '$input_nhx' relax_input.nhx &&
         echo $gencodeid > tool_params &&
         echo `pwd`/relax_input.fa >> tool_params &&
         echo `pwd`/relax_input.nhx >> tool_params &&
-        echo 3 &&
-        echo 2 &&
-        echo $analysisType > tool_params &&
+        echo '3' &&
+        echo '2' &&
+        echo '$analysisType' >> tool_params &&
         @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
     #else:
         ln -s '$input_file' relax_input.fa &&
@@ -24,8 +24,8 @@
         echo $gencodeid > tool_params &&
         echo `pwd`/relax_input.fa >> tool_params &&
         echo `pwd`/relax_input.nhx >> tool_params &&
-        echo 2 &&
-        echo $analysisType > tool_params &&
+        echo '2' &&
+        echo '$analysisType' > tool_params &&
         @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
     #end if
     ]]>