<?xml version="1.0"?>
<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0">
    <description>Detect relaxed selection in a codon-based phylogenetic framework</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 $treeAnnotations == 2:
        ln -s '$input_file' relax_input.fa &&
        ln -s '$input_nhx' relax_input.nhx &&
        echo $gencodeid > tool_params &&
        echo `pwd`/relax_input.fa >> tool_params &&
        echo `pwd`/relax_input.nhx >> tool_params &&
        echo '3' &&
        echo '2' &&
        echo '$analysisType' >> tool_params &&
        @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
    #else:
        ln -s '$input_file' relax_input.fa &&
        ln -s '$input_nhx' relax_input.nhx &&
        echo $gencodeid > tool_params &&
        echo `pwd`/relax_input.fa >> tool_params &&
        echo `pwd`/relax_input.nhx >> tool_params &&
        echo '2' &&
        echo '$analysisType' > tool_params &&
        @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
    #end if
    ]]>
    </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" />
        <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>
        <param name="analysisType" type="select" label="Analysis Type">
            <option value="1">All</option>
            <option value="2">Minimal</option>
        </param>
        <param name="treeAnnotations" type="select" label="Tree Annotations">
            <option value="1">TEST only</option>
            <option value="2">TEST and REFERENCE</option>
        </param>
    </inputs>
    <outputs>
        <data name="relax_log" format="txt" />
        <data name="relax_output" format="json" from_work_dir="relax_input.fa.RELAX.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="relax-in1.fa" />
            <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" />
            <output name="relax_output" file="relax-out1.json" compare="sim_size" />
        </test>
    </tests>
    <help>
        <![CDATA[
RELAX (Detect relaxed selection in a codon-based phylogenetic framework)
        ]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>
</tool>