Mercurial > repos > kpbioteam > clusterprofiler_go

changeset 8:24b134d07b1b draft

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Deleted selected files
author kpbioteam
date Mon, 29 Apr 2019 12:35:33 -0400
parents e92aff6cd674
children 434b5ea29183
files clusterProfiler_go.xml
diffstat 1 files changed, 0 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/clusterProfiler_go.xml	Sun Apr 28 13:57:57 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<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>