view hyphy_absrel.xml @ 0:419cd817299c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea

<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
    <![CDATA[
    ln -s '$input_file' absrel_input.fa &&
    ln -s '$input_nhx' absrel_input.nhx &&
    echo $gencodeid > tool_params &&
    echo `pwd`/absrel_input.fa >> tool_params &&
    echo `pwd`/absrel_input.nhx >> tool_params &&
    echo '$branches' >> tool_params &&
    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
    #if $log:
        > '$absrel_log'
    #end if
    ]]>
    </command>
    <inputs>
        <expand macro="inputs" />
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />
        <expand macro="gencode" />
        <expand macro="branches" />
    </inputs>
    <outputs>
        <data name="absrel_log" format="txt">
            <filter>log</filter>
        </data>
        <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
            <param name="log" value="false" />
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
        </test>
    </tests>
    <help>
        <![CDATA[
aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
        ]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>
</tool>