Mercurial > repos > rdvelazquez > hyphy_relax

diff hyphy_relax.xml @ 9:186972ed2a15 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:21:21 -0400
parents 91e554a9ced6
children
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line diff
--- a/hyphy_relax.xml	Mon Feb 18 15:16:35 2019 -0500
+++ b/hyphy_relax.xml	Fri Jun 07 10:21:21 2019 -0400
@@ -1,40 +1,32 @@
 <?xml version="1.0"?>
-<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0">
+<tool id="hyphy_relax" name="HyPhy-RELAX" version="2.5.0+galaxy0">
   <description>Detect relaxed selection in a codon-based
   phylogenetic framework</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="version_command"/>
   <command detect_errors="exit_code"><![CDATA[
-      #if $treeAnnotations == "2":
-        ln -s '$input_file' relax_input.fa &&
-        ln -s '$input_nhx' relax_input.nhx &&
-        echo $gencodeid > tool_params &&
-        echo `pwd`/relax_input.fa >> tool_params &&
-        echo `pwd`/relax_input.nhx >> tool_params &&
-        echo '3' >> tool_params &&
-        echo '2' >> tool_params &&
-        echo '$analysisType' >> tool_params &&
-        @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
-      #else:
-        ln -s '$input_file' relax_input.fa &&
-        ln -s '$input_nhx' relax_input.nhx &&
-        echo $gencodeid > tool_params &&
-        echo `pwd`/relax_input.fa >> tool_params &&
-        echo `pwd`/relax_input.nhx >> tool_params &&
-        echo '2' >> tool_params &&
-        echo '$analysisType' >> tool_params &&
-        @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
-      #end if
+      ln -s '$input_file' relax_input.fa &&
+      ln -s '$input_nhx' relax_input.nhx &&
+      @HYPHY_INVOCATION@ relax
+        --alignment `pwd`/relax_input.fa
+        --tree `pwd`/relax_input.nhx
+        --models '$analysisType'
+        #if $treeAnnotations == "2":
+          --test TEST
+          --reference REFERENCE
+        #else:
+          --test TEST
+        #end if
+        > '$relax_log'
     ]]></command>
   <inputs>
     <expand macro="inputs"/>
     <expand macro="gencode"/>
     <param name="analysisType" type="select" label="Analysis Type">
-      <option value="1">All</option>
-      <option value="2">Minimal</option>
+      <option value="All">All</option>
+      <option value="Minimal">Minimal</option>
     </param>
     <param name="treeAnnotations" type="select" label="Tree Annotations">
       <option value="1">TEST only</option>