# HG changeset patch
# User rdvelazquez
# Date 1559917219 14400
# Node ID 9640a5b5150237896054fec38192506407e6576b
# Parent  876a69d2c6d78cec6a126f25b4f77980f6abd29e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty

diff -r 876a69d2c6d7 -r 9640a5b51502 hyphy_gard.xml
--- a/hyphy_gard.xml	Thu Mar 21 06:08:04 2019 -0400
+++ b/hyphy_gard.xml	Fri Jun 07 10:20:19 2019 -0400
@@ -1,33 +1,29 @@
 <?xml version="1.0"?>
-<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0">
+<tool id="hyphy_gard" name="HyPhy-GARD" version="2.5.0+galaxy0">
   <description>: Recombination Detection</description>
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements">
-    <requirement type="package" version="1.0.4">translate-gard</requirement>
-  </expand>
-  <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
-  <command detect_errors="exit_code"><![CDATA[
-    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-2} &&
+  <command detect_errors="exit_code">
+  <![CDATA[
     ln -s '$input_file' gard_input.fa &&
-    echo `pwd`/gard_input.fa > tool_params &&
-    echo "010010" >> tool_params &&
-    echo $rate_cond.rate >> tool_params &&
-    #if str($rate_cond.rate) != "1":
-        echo $rate_cond.rate_classes >> tool_params &&
-    #end if
-    echo `pwd`/"gard_input.GARD" >> tool_params &&
-    @HYPHYMPI_INVOCATION@ \$HYPHYMPI_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' &&
-    translate-gard -i gard_input.GARD -j gard_input.GARD.json -o gard_input.fa.translated.json
+    @HYPHY_INVOCATION@ gard
+      --alignment `pwd`/gard_input.fa
+      --type 
+      --code
+      --model
+      --rv '$rate'
+      --rate-classes '$rate_classes'
+
+      > '$gard_log' &&
     ]]></command>
   <inputs>
     <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
     <conditional name="rate_cond">
       <param name="rate" type="select" label="Rate variation">
-        <option value="1">None</option>
-        <option value="2">General Discrete</option>
-        <option value="3">Beta-Gamma</option>
+        <option value="None">None</option>
+        <option value="GDD">General Discrete</option>
+        <option value="Gamma">Beta-Gamma</option>
       </param>
       <when value="1"/>
       <when value="2">
diff -r 876a69d2c6d7 -r 9640a5b51502 macros.xml
--- a/macros.xml	Thu Mar 21 06:08:04 2019 -0400
+++ b/macros.xml	Fri Jun 07 10:20:19 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>