comparison macros.xml @ 8:4e7f1a7d18be draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954

7:f3e408cc2546

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.5.36</token>
    <xml name="inputs">
	    <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
        <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">HyPhy</xref>
        </xrefs>
    </xml>
    <xml name="substitution">
        <param name="model" type="select" label="Substitution model">
            <option value="GTR">GTR - General time reversible
            model</option>
            <option value="LG">LG - Generalist empirical model from
            Le and Gascuel (2008)</option>
            <option value="HIVBm">HIVBm - Specialist empirical model

            #end if
    </token>

    <xml name="mcmc_options">
        <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
        <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
        <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
        <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
    </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>

        </conditional>
    </xml>

    <xml name="branches">
        <conditional name="branch_cond">
            <param name="branch_sel" 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>
                <option value="specify">Enter a branch label</option>

            <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="alternative_model_output">
        <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
            <filter>advanced['save_alternative_model']</filter>
        </data>
    </xml>
    <xml name="resample">
        <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." />

            --starting-points $advanced.starting_points
            --syn-rates $advanced.syn_rates
            --rates $advanced.rates
            --srv $advanced.srv
            #if $advanced.save_alternative_model:
                --save-fit alternative_model.json
            #end if
        #end if
    ]]></token>
    <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
    <token name="@ERRORS@"><![CDATA[

8:4e7f1a7d18be

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.5.47</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.05</token>

    <xml name="inputs">
	    <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
        <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">HyPhy</xref>
        </xrefs>
    </xml>
    <xml name="substitution" tokens="argument">
        <param argument="@ARGUMENT@" type="select" label="Substitution model">
            <option value="GTR">GTR - General time reversible
            model</option>
            <option value="LG">LG - Generalist empirical model from
            Le and Gascuel (2008)</option>
            <option value="HIVBm">HIVBm - Specialist empirical model

            #end if
    </token>

    <xml name="mcmc_options">
        <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
        <param argument="--chain-length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
        <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
        <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
    </xml>

    <xml name="gencode">
        <param argument="--code" 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>

        </conditional>
    </xml>

    <xml name="branches">
        <conditional name="branch_cond">
            <param argument="--branches" name="branch_sel" 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>
                <option value="specify">Enter a branch label</option>

            <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="alternative_model_output">
        <data name="alternative_model" format="nhx" from_work_dir="alternative_model.nhx" label="${tool.name} on ${on_string}: Alternative model">
            <filter>advanced['save_alternative_model']</filter>
        </data>
    </xml>
    <xml name="resample">
        <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." />

            --starting-points $advanced.starting_points
            --syn-rates $advanced.syn_rates
            --rates $advanced.rates
            --srv $advanced.srv
            #if $advanced.save_alternative_model:
                --save-fit alternative_model.nhx
            #end if
        #end if
    ]]></token>
    <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
    <token name="@ERRORS@"><![CDATA[