view hyphy_relax.xml @ 3:0648b03f1d2f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 20:18:43 -0500
parents f078fc88982d
children 7782bb7bc7b7
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<?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" />
    <expand macro="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 $gencodeid > tool_params &&
        echo `pwd`/relax_input.fa >> tool_params &&
        echo `pwd`/relax_input.nhx >> tool_params &&
	echo '$treeAnnotations' >> 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 $gencodeid > tool_params &&
        echo `pwd`/relax_input.fa >> tool_params &&
        echo `pwd`/relax_input.nhx >> tool_params &&
	echo '$treeAnnotations' >> tool_params &&
        echo '2' &&
        echo '$analysisType' >> tool_params &&
        @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
      #end if
    ]]>
    </command>
    <inputs>
        <expand macro="inputs" />
        <expand macro="gencode" />
        <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="hyphy_json_results" 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/msu400</citation>
    </expand>
</tool>