Mercurial > repos > kpbioteam > clusterprofiler_kegg
changeset 0:a6873f1cdc20 draft default tip
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_kegg commit 48b6e9100e15087e16606d808b578fdd39868f7e-dirty
| author | kpbioteam |
|---|---|
| date | Wed, 02 May 2018 12:00:05 -0400 |
| parents | |
| children | |
| files | README.md clusterProfiler_kegg.R clusterprofiler_kegg.xml gene.txt kegg.txt test-data/gene.txt test-data/kegg.txt |
| diffstat | 7 files changed, 44 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed May 02 12:00:05 2018 -0400 @@ -0,0 +1,1 @@ +# clusterProfiler_kegg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clusterProfiler_kegg.R Wed May 02 12:00:05 2018 -0400 @@ -0,0 +1,12 @@ +require("clusterProfiler", quietly = TRUE) + +args <- commandArgs(trailingOnly = TRUE) + +input1 = args[1] +output = args[2] + +gene <- c(read.table(input1)) +kk <- enrichKEGG(gene = gene, + organism = 'hsa') + +write.table(kk, output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clusterprofiler_kegg.xml Wed May 02 12:00:05 2018 -0400 @@ -0,0 +1,27 @@ +<tool id="clusterprofiler_kegg" name="clusterProfiler_kegg" version="0.1.0"> + <description>run KEGG Analysis</description> + <requirements> + <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript ${__tool_directory__}/clusterProfiler_kegg.R "$input1" "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="txt" /> + </inputs> + <outputs> + <data name="output1" format="txt" /> + </outputs> + <tests> + <test> + <param name="input1" value="gene.txt"/> + <output name="output1" file="kegg.txt"/> + </test> + </tests> + <help><![CDATA[ + KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control. + ]]></help> + <citations> + <citation type="doi">10.1089/omi.2011.0118</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gene.txt Wed May 02 12:00:05 2018 -0400 @@ -0,0 +1,1 @@ + "5319", "53347", "53637", "5467", "54768", "54798", "54801", "55800", "56649", "56926", "57348"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg.txt Wed May 02 12:00:05 2018 -0400 @@ -0,0 +1,1 @@ +"ID" "Description" "GeneRatio" "BgRatio" "pvalue" "p.adjust" "qvalue" "geneID" "Count"