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clusterProfiler_go.xml |
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| diff -r 2bc8aa30b9db -r e92aff6cd674 clusterProfiler_go.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clusterProfiler_go.xml Sun Apr 28 13:57:57 2019 -0400 |
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| @@ -0,0 +1,56 @@ +<tool id="clusterprofiler_go" name="Cluster Profiler GO" version="0.1.0"> + <description>run GO Analysis</description> + <requirements> + <requirement type="package" version="3.10.1">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> |