comparison cummeRbund_macros.xml @ 0:587c425b4e76 draft

Initial commit with version 1.0.0 of the cummeRbund wrapper.

0:587c425b4e76

<?xml version="1.0"?>
<macros>
    <macro name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </macro>
    <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.dataset.file_name)" />
        <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
    </macro>
    <macro name="genes_selector">
        <repeat name="genes" title="Genes">
            <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.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>