# HG changeset patch
# User rdvelazquez
# Date 1559917065 14400
# Node ID 3fcbbe88b6d82ec1133d028bc22182922be1902d
# Parent  5b00c7f5b03d17c16f77fa3f653cc3b829ca240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty

diff -r 5b00c7f5b03d -r 3fcbbe88b6d8 hyphy_bgm.xml
--- a/hyphy_bgm.xml	Tue Mar 05 20:13:34 2019 -0500
+++ b/hyphy_bgm.xml	Fri Jun 07 10:17:45 2019 -0400
@@ -1,39 +1,35 @@
 <?xml version="1.0"?>
-<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
+<tool id="hyphy_bgm" name="HyPhy-BGM" version="2.5.0+galaxy0">
   <description>- Detecting coevolving sites via Bayesian graphical models</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
   <command detect_errors="exit_code"><![CDATA[
     ln -s '$input_file' bgm_input.fa &&
     ln -s '$input_nhx' bgm_input.nhx &&
-    echo '$datatype.value' > tool_params &&
-    #if str($datatype.value) == "3":
-      echo '$datatype.gencodeid' >> tool_params &&
-    #end if
-    echo `pwd`/bgm_input.fa >> tool_params &&
-    #if str($datatype.value) == "2":
-      echo '$datatype.model' >> tool_params &&
-    #end if
-    echo `pwd`/bgm_input.nhx >> tool_params &&
-    echo '$branch_subset' >> tool_params &&
-    echo '$chain_length' >> tool_params &&
-    echo '$burn_in' >> tool_params &&
-    echo '$sample' >> tool_params &&
-    echo '$parents' >> tool_params &&
-    echo '$min_subs' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/BGM.bf > '$bgm_log'
+    @HYPHY_INVOCATION@ bgm
+      --alignment `pwd`/bgm_input.fa
+      --tree `pwd`/bgm_input.nhx
+      --run_type $datatype.value
+      --code '$datatype.gencodeid'
+      --baseline_model '$datatyupe.model'
+      --branches '$branch_subset'
+      --chain '$chain_length'
+      --burn_in '$burn_in'
+      --samples '$samples'
+      --parents '$parents'
+      --min_subs '$min_sumbs'
+      > '$bgm_log'
     ]]></command>
   <inputs>
     <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
     <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
     <conditional name="datatype">
       <param name="value" type="select" label="Type of data">
-        <option value="1">Nucleotide</option>
-        <option value="2">Amino acid</option>
-        <option value="3">Codon</option>
+        <option value="nucleotide">Nucleotide</option>
+        <option value="amino-acid">Amino acid</option>
+        <option value="codon">Codon</option>
       </param>
       <when value="1">
       </when>
diff -r 5b00c7f5b03d -r 3fcbbe88b6d8 macros.xml
--- a/macros.xml	Tue Mar 05 20:13:34 2019 -0500
+++ b/macros.xml	Fri Jun 07 10:17:45 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>