<tool id="clusterprofiler_go" name="Cluster Profiler GO" version="0.1.0">
    <description>run GO Analysis</description>
    <requirements>
        <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement>
        <requirement type="package">r-ggplot2</requirement>
        <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
    </requirements>
<command detect_errors="exit_code"><![CDATA[
        Rscript '$clusterprofiler_go_script'
    ]]></command>
    <configfiles>
        <configfile name="clusterprofiler_go_script"><![CDATA[

require("clusterProfiler", quietly = TRUE)
require("org.Hs.eg.db", quietly = TRUE)
require("ggplot2", quietly = TRUE)

gene <- read.table('$entrezid')
ego <- enrichGO(gene          = c(gene\$V2),
                keyType = "ENTREZID",
                OrgDb         = org.Hs.eg.db,
                ont           = "BP",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
                readable      = TRUE)                

write.table(ego, '$table')
dotplot(ego)
ggsave(file = '$plot', device = "pdf")

        ]]>
        </configfile>
    </configfiles> 
        
    <inputs>
        <param type="data" name="entrezid" format="txt" />
    </inputs>
    <outputs>
        <data name="table" format="txt" />
        <data name="plot" format="pdf" />
    </outputs>
    <tests>
        <test>
            <param name="entrezid" value="genedf.txt"/>
            <output name="table" file="ego.txt"/>
            <output name="plot" file="ego.pdf"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool provide GO Enrichment Analysis of a gene set. Given a set of genes, this will return the enrichment GO categories after FDR control.
    ]]></help>
    <citations>
        <citation type="doi">10.1089/omi.2011.0118</citation>
    </citations>
</tool>