annotate peca.xml @ 12:5c3b60c36c66 draft

planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca

<tool id="peca" name="PECA" version="0.1.2">
    <description>probe-level expression change averaging</description>
    <requirements>
        <requirement type="package" version="1.14.0">bioconductor-peca</requirement>
        <requirement type="package" version="3.4.1">r-base</requirement>
        <requirement type="package">r-dbi</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## write groups to file
        echo '$group1' > group1.txt &&
        echo '$group2' > group2.txt && 
        Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$paired' '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular"/>
        <param name="group1" type="data_column" data_ref="input" multiple="true"/>
        <param name="group2" type="data_column" data_ref="input" multiple="true"/> 
        <param name="test_type" type="select" label="Type of test">
            <option value="t" selected="true">Standard t-test</option>
            <option value="modt">Modified t-test</option>
            <option value="rots">Reproducibility-optimized test statistic</option>
        </param>
        <param name="paired" type="boolean" label="Perform paired t-test" checked="false"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test.tab" ftype="tabular"/>
            <param name="group1" value="2,3,4"/>
            <param name="group2" value="5,6,7"/>
            <param name="test_type" value="t"/>
            <param name="paired" value="false"/>
            <output name="output" file="out.tab" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
</tool>