annotate charts.xml @ 63:193e4c6c49ea draft

Uploaded

<tool id="charts" name="Charts" version="1.0.0">
    <hidden>True</hidden>
    <description>wrapper for R</description>
    <requirements>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
        <requirement type="package" version="3.0.3">R</requirement>
        <requirement type="package" version="1.0">charts_r_packages</requirement>
    </requirements>
    <command>Rscript \$SCRIPT_PATH/charts.r -w \$SCRIPT_PATH/ -m ${module} -i ${input} -c '${columns}' -s '${settings}' -o ${output}
    </command>
    <inputs>
        <param name="input" type="data" label="Input dataset" format="tabular" />
        <param name="module" type="select" label="R-script">
            <option value="boxplot">boxplot</option>
            <option value="heatmap">heatmap</option>
            <option value="histogram">histogram</option>
            <option value="histogramdiscrete">histogramdiscrete</option>
        </param>
        <param name="columns" type="text" label="Columns string (i.e key1: column, key2: column)" value="column: 2"/>
        <param name="settings" type="text" label="Options string (i.e data_limit: 1000)" value=""/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="tabular.txt" />
            <param name="module" value="histogram" />
            <param name="columns" value="key1: 2" />
            <param name="settings" value="" />
            <output name="output" file="histogram.000.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular.txt" />
            <param name="module" value="histogram" />
            <param name="columns" value="key1: 2, key2: 3, key3: 4" />
            <param name="settings" value="" />
            <output name="output" file="histogram.001.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular_data.txt" />
            <param name="module" value="histogram" />
            <param name="columns" value="key1: 6" />
            <param name="settings" value="" />
            <output name="output" file="histogram.002.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular_single.txt" />
            <param name="module" value="histogram" />
            <param name="columns" value="key1: 1" />
            <param name="settings" value="" />
            <output name="output" file="histogram.003.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular.txt" />
            <param name="module" value="boxplot" />
            <param name="columns" value="key1: 2" />
            <param name="settings" value="" />
            <output name="output" file="boxplot.000.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular.txt" />
            <param name="module" value="boxplot" />
            <param name="columns" value="key1: 2, key2: 3, key3: 4" />
            <param name="settings" value="" />
            <output name="output" file="boxplot.001.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular_matrix.txt" />
            <param name="module" value="histogramdiscrete" />
            <param name="columns" value="key1: 1, key2: 2, key3: 3" />
            <param name="settings" value="" />
            <output name="output" file="histogramdiscrete.000.txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="tabular_matrix.txt" />
            <param name="module" value="heatmap" />
            <param name="columns" value="key1: 1, key2: 2, key3: 3" />
            <param name="settings" value="" />
            <output name="output" file="heatmap.000.txt" lines_diff="2"/>
        </test>
    </tests>
</tool>