Mercurial > repos > rdvelazquez > hyphy_fubar

diff hyphy_fubar.xml @ 12:8600d5c4e466 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 10:19:48 -0400
parents da4fd8c3ad0c
children
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--- a/hyphy_fubar.xml	Mon Feb 18 15:17:18 2019 -0500
+++ b/hyphy_fubar.xml	Fri Jun 07 10:19:48 2019 -0400
@@ -1,26 +1,26 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0">
+<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="2.5.0+galaxy0">
     <description>Fast Unconstrained Bayesian AppRoximation</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="version_command" />
     <command detect_errors="exit_code">
     <![CDATA[
     ln -s '$input_file' fubar_input.fa &&
     ln -s '$input_nhx' fubar_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/fubar_input.fa >> tool_params &&
-    echo `pwd`/fubar_input.nhx >> tool_params &&
-    echo '$grid_points' >> tool_params &&
-    echo '$posterior' >> tool_params &&
-    echo '$mcmc' >> tool_params &&
-    echo '$chain_length' >> tool_params &&
-    echo '$samples' >> tool_params &&
-    echo '$samples_per_chain' >> tool_params &&
-    echo '$concentration' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf > '$fubar_log'
+    @HYPHY_INVOCATION@ fubar
+        --alignment `pwd`/fubar_input.fa
+        --tree `pwd`/fubar_input.nhx
+        --code '$gencodeid'
+        --method '$posterior'
+        --grid '$grid_points'
+        --chains '$mcmc'
+        --chain-length '$chain_length'
+        --burn-in '$samples'
+        --samples '$samples_per_chain'
+        --concentration_parameter '$concentration'
+        > '$fubar_log'
     ]]>
     </command>
     <inputs>
@@ -28,9 +28,9 @@
         <expand macro="gencode" />
         <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" />
         <param name="posterior" type="select" label="Posterior estimation method">
-            <option value="1">Full Metropolis-Hastings MCMC algorithm</option>
-            <option value="2">Collapsed Gibbs sampler</option>
-            <option value="3">0-th order Variational Bayes approximations</option>
+            <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
+            <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
+            <option value="Variational-Bayes">0-th order Variational Bayes approximations</option>
         </param>
         <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
         <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />