# HG changeset patch
# User rdvelazquez
# Date 1559917188 14400
# Node ID 8600d5c4e466596615031087b9735608b0ea30e9
# Parent  ca2c7c484990bb1cc7321f0f010d531025fbc1de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty

diff -r ca2c7c484990 -r 8600d5c4e466 hyphy_fubar.xml
--- 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" />
diff -r ca2c7c484990 -r 8600d5c4e466 macros.xml
--- a/macros.xml	Mon Feb 18 15:17:18 2019 -0500
+++ b/macros.xml	Fri Jun 07 10:19:48 2019 -0400
@@ -6,50 +6,43 @@
   </xml>
   <xml name="gencode">
     <param name="gencodeid" type="select" label="Genetic code">
-      <option value="1">Universal code</option>
-      <option value="2">Vertebrate mitochondrial DNA code</option>
-      <option value="3">Yeast mitochondrial DNA code</option>
-      <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
-      <option value="5">Invertebrate mitochondrial DNA code</option>
-      <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
-      <option value="7">Echinoderm mitochondrial DNA code</option>
-      <option value="8">Euplotid Nuclear code</option>
-      <option value="9">Alternative Yeast Nuclear code</option>
-      <option value="10">Ascidian mitochondrial DNA code</option>
-      <option value="11">Flatworm mitochondrial DNA code</option>
-      <option value="12">Blepharisma Nuclear code</option>
+      <option value="Universal">Universal code</option>
+      <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA code</option>
+      <option value="Yeast-mtDNA">Yeast mitochondrial DNA code</option>
+      <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
+      <option value="Invertebrate-mtDNA">Invertebrate mitochondrial DNA code</option>
+      <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
+      <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA code</option>
+      <option value="Euplotid-Nuclear">Euplotid Nuclear code</option>
+      <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear code</option>
+      <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA code</option>
+      <option value="Flatworm-mtDNA,">Flatworm mitochondrial DNA code</option>
+      <option value="Blepharisma-Nuclear">Blepharisma Nuclear code</option>
     </param>
   </xml>
   <xml name="branches">
     <param name="branches" type="select" label="Set of branches to test">
-      <option value="1">All branches</option>
-      <option value="2">Internal branches</option>
-      <option value="3">Leaf branches</option>
-      <option value="4">Unlabeled branches</option>
+      <option value="All">All branches</option>
+      <option value="Internal">Internal branches</option>
+      <option value="Leaves">Leaf branches</option>
+      <option value="'Unlabeled-branches'">Unlabeled branches</option>
     </param>
   </xml>
-  <xml name="version_command">
-    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
-  </xml>
   <xml name="citations">
     <citations>
       <citation type="doi">10.1093/bioinformatics/bti079</citation>
       <yield/>
     </citations>
   </xml>
-  <token name="@VERSION@">2.3.14</token>
+  <token name="@VERSION@">2.5.0</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@VERSION@">hyphy</requirement>
       <yield/>
     </requirements>
   </xml>
-  <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
+  <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
 export HYPHY_PATH=`dirname \$HYPHY` &&
 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
-  <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
-  <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
-export HYPHYMPI_PATH=`dirname \$HYPHYMPI` &&
-export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
-cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
+  <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | hyphy LIBPATH=\$HYPHY_LIB ]]></token>
 </macros>