<?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="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="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="citations">
    <citations>
      <citation type="doi">10.1093/bioinformatics/bti079</citation>
      <yield/>
    </citations>
  </xml>
  <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 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 | hyphy LIBPATH=\$HYPHY_LIB ]]></token>
</macros>
