<?xml version="1.0"?>
<macros>
  <xml name="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"/>
  </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>
    </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>
    </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>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@VERSION@">hyphy</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
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>
</macros>