# HG changeset patch
# User rdvelazquez
# Date 1559917127 14400
# Node ID 4377e155b9d1453f70bb023e543510b7d4880d31
# Parent  070a1988e661d176880061a19d96a470e0ee81bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty

diff -r 070a1988e661 -r 4377e155b9d1 hyphy_fade.xml
--- a/hyphy_fade.xml	Mon Feb 18 15:11:29 2019 -0500
+++ b/hyphy_fade.xml	Fri Jun 07 10:18:47 2019 -0400
@@ -1,41 +1,27 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
+<tool id="hyphy_fade" name="HyPhy-FADE" version="2.5.0+galaxy0">
   <description>: FUBAR* Approach to Directional Evolution (*Fast
   Unconstrained Bayesian Approximation)</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>HYPHYMP --version | tail -n 1 | awk '{print
-  $1}'</version_command>
   <command detect_errors="exit_code"><![CDATA[
-    #if $posteriorEstimationMethod == 3:
-      ln -s '$input_file' fade_input.fa &&
-      ln -s '$input_nhx' fade_input.nhx &&
-      echo `pwd`/fade_input.fa >> tool_params &&
-      echo `pwd`/fade_input.nhx >> tool_params &&
-      echo '$branches' >> tool_params &&
-      echo '$grid_points' >> tool_params &&
-      echo '$substitutionmodel' >> tool_params &&
-      echo '$posteriorEstimationMethod' >> tool_params &&
-      echo '$concentration' >> tool_params &&
-      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
-    #else:
-      ln -s '$input_file' fade_input.fa &&
-      ln -s '$input_nhx' fade_input.nhx &&
-      echo `pwd`/fade_input.fa >> tool_params &&
-      echo `pwd`/fade_input.nhx >> tool_params &&
-      echo '$branches' >> tool_params &&
-      echo '$grid_points' >> tool_params &&
-      echo '$substitutionmodel' >> tool_params &&
-      echo '$posteriorEstimationMethod' >> tool_params &&
-      echo '$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/FADE.bf > '$fade_log'
-    #end if
+    ln -s '$input_file' fade_input.fa &&
+    ln -s '$input_nhx' fade_input.nhx &&
+    @HYPHY_INVOCATIN@ fade
+      --alignment `pwd`/fade_input.fa
+      --tree `pwd`/fade_input.nhx
+      --branches '$branches'
+      --model '$substitutionmodel'
+      --method '$posteriorEstimationMethod'
+      --grid '$grid_points'
+      --concentration_parameter '$concentration'
+      --chains '$mcmc'
+      --chain-length '$chain_length'
+      --burn-in '$samples'
+      --samples '$samples_per_chain'
+      > '$fade_log'
     ]]></command>
   <inputs>
     <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
diff -r 070a1988e661 -r 4377e155b9d1 macros.xml
--- a/macros.xml	Mon Feb 18 15:11:29 2019 -0500
+++ b/macros.xml	Fri Jun 07 10:18:47 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>