annotate peca.xml @ 0:f50bb34c1a37 draft

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

<tool id="peca" name="PECA: Probe-level expression change averaging" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.14.0">bioconductor-peca</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## write group 1 to file
        echo '$group1' > group1.txt &&
        echo '$group2' > group2.txt && 
        cat group1.txt &&
        Rscript --vanilla '$__tool_directory__/peca.R' '$input' '$group1' '$group2' '$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"/> 
    </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="4,5,6"/>
            <output name="output" file="out.tab" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
</tool>