Mercurial > repos > rdvelazquez > hyphy_meme

diff hyphy_meme.xml @ 3:f84a42d3ef98 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 10:20:49 -0400
parents cffd8bd6e3ec
children
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--- a/hyphy_meme.xml	Mon Feb 18 15:15:12 2019 -0500
+++ b/hyphy_meme.xml	Fri Jun 07 10:20:49 2019 -0400
@@ -1,22 +1,21 @@
 <?xml version="1.0"?>
-<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
+<tool id="hyphy_meme" name="HyPhy-MEME" version="2.5.0+galaxy0">
     <description>: Mixed Effects Model of Evolution</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="version_command" />
     <command detect_errors="exit_code">
     <![CDATA[
-    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
-    ln -s '$input_file' meme_input.fa &&
-    ln -s '$input_nhx' meme_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/meme_input.fa >> tool_params &&
-    echo `pwd`/meme_input.nhx >> tool_params &&
-    echo $branches >> tool_params &&
-    echo $p_value >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
+        ln -s '$input_file' meme_input.fa &&
+        ln -s '$input_nhx' meme_input.nhx &&
+        @HYPHY_INVOCATION@ meme
+            --alignment `pwd`/meme_input.fa
+            --tree `pwd`/meme_input.nhx
+            --code '$gencodeid'
+            --branches '$branches'
+            --pvalue '$p_value'
+            > '$meme_log'
     ]]>
     </command>
     <inputs>