comparison hyphy_cfel.xml @ 2:fb833dd994f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

1:710fdaa85384

<?xml version="1.0"?>
<tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy0" profile="19.09">
    <description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' cfel_input.fa &&
        ln -s '$input_nhx' cfel_input.nhx &&
        hyphy contrast-fel
            --code '$gencodeid'
            #for branch in str($branch_set).split(','):
                --branch-set '$branch'
            #end for
            --srv '$srv'
            --permutations '$permutations'
            --pvalue '$pvalue'
            --qvalue '$qvalue'
            --output '$cfel_output'
            cfel_input.fa
            cfel_input.nhx
            > '$cfel_log'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param argument="--branch-set" type="select" multiple="true" min="2" max="2" label="Set of branches to test">
            <option value="Internal branches">Internal branches</option>
            <option value="Terminal branches">Terminal branches</option>
            <option value="Random set of branches">Random set of branches</option>
            <option value="Unlabeled branches">Unlabeled branches</option>
        </param>
        <param argument="--permutations" type="boolean" truevalue="Yes" falsevalue="No" label="Perform permutation significance tests"/>
        <param argument="--pvalue" type="float" value=".05" min="0" max="1" label="Significance value for site-tests"/>
        <param argument="--qvalue" type="float" value=".2" min="0" max="1" label="Significance value for FDR reporting"/>
        <param argument="--srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
            <option value="Yes">Yes (recommended)</option>
            <option value="No">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="cfel_log" format="txt"/>
        <data name="cfel_output" format="hyphy_results.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="branch_set" value="Internal branches,Terminal branches" />
            <output name="cfel_output" file="cfel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Contrast-FEL : A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

2:fb833dd994f2

<?xml version="1.0"?>
<tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy1" profile="19.09">
    <description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy contrast-fel
            --code '$gencodeid'
            #for $i, $branch in enumerate($branch_repeat):
                --branch-set '$branch.branch_label'
            #end for
            --srv '$srv'
            --permutations '$permutations'
            --pvalue '$pvalue'
            --qvalue '$qvalue'
            --output '$cfel_output'
            $input_file
            @INPUT_TREE@
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <repeat name="branch_repeat" title="Branch set" min="2">
            <param name="branch_label" type="text" value="Test" optional="false" label="Label for set">
                <sanitizer invalid_char="">
                    <valid initial="default" />
                </sanitizer>
            </param>
        </repeat>
        <param argument="--permutations" type="boolean" truevalue="Yes" falsevalue="No" label="Perform permutation significance tests"/>
        <param argument="--pvalue" type="float" value=".05" min="0" max="1" label="Significance value for site-tests"/>
        <param argument="--qvalue" type="float" value=".2" min="0" max="1" label="Significance value for FDR reporting"/>
        <param argument="--srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
            <option value="Yes">Yes (recommended)</option>
            <option value="No">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="cfel_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <repeat name="branch_repeat">
                <param name="branch_label" value="Internal branches" />
            </repeat>
            <repeat name="branch_repeat">
                <param name="branch_label" value="Terminal branches" />
            </repeat>
            <output name="cfel_output" file="cfel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Contrast-FEL : A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches