comparison clusterProfiler_go.xml @ 0:d81d0f7d99a6 draft

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author kpbioteam
date Sun, 28 Apr 2019 03:43:14 -0400
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1 <tool id="clusterprofiler_go" name="Cluster Profiler GO" version="0.1.0">
2 <description>run GO Analysis</description>
3 <requirements>
4 <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement>
5 <requirement type="package">r-ggplot2</requirement>
6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$clusterprofiler_go_script'
10 ]]></command>
11 <configfiles>
12 <configfile name="clusterprofiler_go_script"><![CDATA[
13
14 require("clusterProfiler", quietly = TRUE)
15 require("org.Hs.eg.db", quietly = TRUE)
16 require("ggplot2", quietly = TRUE)
17
18 gene <- read.table('$entrezid')
19 ego <- enrichGO(gene = c(gene\$V2),
20 keyType = "ENTREZID",
21 OrgDb = org.Hs.eg.db,
22 ont = "BP",
23 pAdjustMethod = "BH",
24 pvalueCutoff = 0.01,
25 qvalueCutoff = 0.05,
26 readable = TRUE)
27
28 write.table(ego, '$table')
29 dotplot(ego)
30 ggsave(file = '$plot', device = "pdf")
31
32 ]]>
33 </configfile>
34 </configfiles>
35
36 <inputs>
37 <param type="data" name="entrezid" format="txt" />
38 </inputs>
39 <outputs>
40 <data name="table" format="txt" />
41 <data name="plot" format="pdf" />
42 </outputs>
43 <tests>
44 <test>
45 <param name="entrezid" value="genedf.txt"/>
46 <output name="table" file="ego.txt"/>
47 <output name="plot" file="ego.pdf"/>
48 </test>
49 </tests>
50 <help><![CDATA[
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.
52 ]]></help>
53 <citations>
54 <citation type="doi">10.1089/omi.2011.0118</citation>
55 </citations>
56 </tool>