Mercurial > repos > kpbioteam > clusterprofiler_go
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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| -1:000000000000 | 0:d81d0f7d99a6 |
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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> |