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1 <tool id="clusterprofiler_go" name="Cluster Profiler GO" version="0.1.0">
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2 <description>run GO Analysis</description>
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3 <requirements>
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4 <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement>
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5 <requirement type="package">r-ggplot2</requirement>
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6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$clusterprofiler_go_script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="clusterprofiler_go_script"><![CDATA[
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13
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14 require("clusterProfiler", quietly = TRUE)
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15 require("org.Hs.eg.db", quietly = TRUE)
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16 require("ggplot2", quietly = TRUE)
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17
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18 gene <- read.table('$entrezid')
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19 ego <- enrichGO(gene = c(gene\$V2),
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20 keyType = "ENTREZID",
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21 OrgDb = org.Hs.eg.db,
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22 ont = "BP",
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23 pAdjustMethod = "BH",
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24 pvalueCutoff = 0.01,
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25 qvalueCutoff = 0.05,
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26 readable = TRUE)
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27
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28 write.table(ego, '$table')
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29 dotplot(ego)
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30 ggsave(file = '$plot', device = "pdf")
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31
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32 ]]>
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33 </configfile>
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34 </configfiles>
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35
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36 <inputs>
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37 <param type="data" name="entrezid" format="txt" />
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38 </inputs>
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39 <outputs>
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40 <data name="table" format="txt" />
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41 <data name="plot" format="pdf" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="entrezid" value="genedf.txt"/>
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46 <output name="table" file="ego.txt"/>
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47 <output name="plot" file="ego.pdf"/>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 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.
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52 ]]></help>
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53 <citations>
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54 <citation type="doi">10.1089/omi.2011.0118</citation>
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55 </citations>
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56 </tool> |
