Mercurial > repos > kpbioteam > clusterprofiler_go

changeset 9:434b5ea29183 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author kpbioteam
date Mon, 29 Apr 2019 12:35:49 -0400
parents 24b134d07b1b
children 5299be80cafb
files clusterProfiler_go.xml
diffstat 1 files changed, 56 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clusterProfiler_go.xml	Mon Apr 29 12:35:49 2019 -0400
@@ -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="3.7.0">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>