Mercurial > repos > rdvelazquez > hyphy_busted

diff hyphy_busted.xml @ 4:f8abbbc7e29e 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 10:18:17 -0400
parents 0d4341fca959
children
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--- a/hyphy_busted.xml	Mon Feb 18 15:14:26 2019 -0500
+++ b/hyphy_busted.xml	Fri Jun 07 10:18:17 2019 -0400
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
-<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
+<tool id="hyphy_busted" name="HyPhy-BUSTED" version="2.5.0+galaxy0">
     <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="version_command" />
     <command detect_errors="exit_code">
     <![CDATA[
     ln -s '$input_file' busted_input.fa &&
     ln -s '$input_nhx' busted_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/busted_input.fa >> tool_params &&
-    echo `pwd`/busted_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf > '$busted_log'
+    @HYPHY_INVOCATION@ busted
+        --alignment `pwd`/busted_input.fa
+        --tree `pwd`/busted_input.nhx
+        --code $gencodeid
+        --branches '$branches'
+        > '$busted_log'
     ]]>
     </command>
     <inputs>