| Previous changeset 7:e92aff6cd674 (2019-04-28) Next changeset 9:434b5ea29183 (2019-04-29) |
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Commit message:
Deleted selected files |
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removed:
clusterProfiler_go.xml |
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| diff -r e92aff6cd674 -r 24b134d07b1b clusterProfiler_go.xml --- a/clusterProfiler_go.xml Sun Apr 28 13:57:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |