view cummeRbund_macros.xml @ 0:962b0ae5939f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty

<?xml version="1.0"?>
<macros>
    <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">
            <options from_dataset="input_database" />
        </param>
        <param name="y" type="select" label="Sample name for y axis">
            <options>
                <filter type="data_meta" ref="input_database" key="samples" />
            </options>
        </param>
    </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">
                <options>
                    <filter type="data_meta" ref="input_database" key="genes" />
                </options>
            </param>
        </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>