comparison hyphy_meme.xml @ 3:3b7f2dbb5c44 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty

2:e44501a5cdcc

    <description>: Mixed Effects Model of Evolution</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
    ln -s '$input_file' meme_input.fa &&
    ln -s '$input_nhx' meme_input.nhx &&

    echo $p_value >> tool_params &&
    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
    ]]>
    </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>
        <conditional name="rate_cond">
            <param name="rate" type="select" label="Rate variation">
                <option value="1">None</option>
                <option value="2">General Discrete</option>
                <option value="3">Beta-Gamma</option>
            </param>
            <when value="1" />
            <when value="2">
                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
            </when>
            <when value="3">
                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
            </when>
        </conditional>
        <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>
        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
    </inputs>
    <outputs>
        <data name="meme_log" format="txt" />
        <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="meme-in1.fa" />
            <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />

3:3b7f2dbb5c44

    <description>: Mixed Effects Model of Evolution</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
    <![CDATA[
    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
    ln -s '$input_file' meme_input.fa &&
    ln -s '$input_nhx' meme_input.nhx &&

    echo $p_value >> tool_params &&
    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
    ]]>
    </command>
    <inputs>
        <expand macro="inputs" />
        <expand macro="gencode" />
        <expand macro="branches" />
        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
    </inputs>
    <outputs>
        <data name="meme_log" format="txt" />
        <data name="meme_output" format="hyphy_json_results" from_work_dir="meme_input.fa.MEME.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="meme-in1.fa" />
            <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />