Mercurial > repos > rdvelazquez > hyphy_absrel

diff hyphy_absrel.xml @ 13:35c1c523ae44 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 10:17:13 -0400
parents edf8263a39cb
children
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--- a/hyphy_absrel.xml	Mon Feb 18 15:13:24 2019 -0500
+++ b/hyphy_absrel.xml	Fri Jun 07 10:17:13 2019 -0400
@@ -1,23 +1,20 @@
 <?xml version="1.0"?>
-<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
-    <description>adaptive Branch Site Random Effects Likelihood</description>
+<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="2.5.0+galaxy0">
+    <description>absrel</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="version_command" />
     <command detect_errors="exit_code">
     <![CDATA[
     ln -s '$input_file' absrel_input.fa &&
     ln -s '$input_nhx' absrel_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/absrel_input.fa >> tool_params &&
-    echo `pwd`/absrel_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
-    #if $log:
+    @HYPHY_INVOCATION@ absrel 
+        --alignment `pwd`/absrel_input.fa
+        --tree `pwd/absrel_input.nhx
+        --code '$gencodeid'
+        --branches '$branches'
         > '$absrel_log'
-    #end if
     ]]>
     </command>
     <inputs>