cummeRbund_macros.xml

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.24.0</token>
    <macro name="replicates_checkbox">
        <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/>
    </macro>
    <macro name="log10_checkbox">
        <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
    </macro>
    <macro name="xy_selector">
        <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.get_file_name())" />
        <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.get_file_name())" />
    </macro>
    <macro name="genes_selector">
        <repeat name="genes" title="Genes" min="2">
            <!-- Cannot create a heatmap for less than two genes -->
            <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.get_file_name())" />
        </repeat>
    </macro>
    <macro name="features_selector">
        <param name="features" type="select" label="Expression levels to plot?">
            <option value="gene" selected="true">Genes</option>
            <option value="isoforms">Isoforms</option>
            <option value="tss">TSS</option>
            <option value="cds">CDS</option>
        </param>
    </macro>
    <macro name="multiple_genes_conditional">
        <conditional name="multiple_genes">
            <param name="multiple_genes_selector" type="select" label="Limit plot to genes">
                <option value="no" selected="true">Do not limit</option>
                <option value="yes">Select genes</option>
            </param>
            <when value="yes">
                <expand macro="features_selector" />
                <expand macro="genes_selector" />
            </when>
            <when value="no" />
        </conditional>
    </macro>
</macros>