Mercurial > repos > proteore > proteore_clusterprofiler
diff cluster_profiler.xml @ 42:3a990910e7f4 draft default tip
"planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty"
| author | proteore |
|---|---|
| date | Fri, 09 Apr 2021 14:38:05 +0000 |
| parents | 3fd1ccc57a6a |
| children |
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--- a/cluster_profiler.xml Fri Dec 06 08:27:03 2019 +0000 +++ b/cluster_profiler.xml Fri Apr 09 14:38:05 2021 +0000 @@ -1,12 +1,13 @@ -<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.12.06"> +<tool id="cluter_profiler" name="Classification and enrichment analysis" version="2021.04.08"> <description>(Human, Mouse, Rat)[clusterProfiler]</description> <requirements> - <requirement type="package">R</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.Rn.eg.db</requirement> - <requirement type="package" version="3.10.2">bioconductor-dose</requirement> - <requirement type="package" version="3.12.0">bioconductor-clusterprofiler</requirement> + <requirement type="package" version="4.0.3">r-base</requirement> + <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="3.12.0">bioconductor-org.rn.eg.db</requirement> + <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement> + <requirement type="package" version="3.16.0">bioconductor-dose</requirement> + <requirement type="package" version="3.18.1">bioconductor-clusterprofiler</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript "$__tool_directory__/GO-enrich.R" @@ -202,12 +203,12 @@ <param name="plot" value="dotplot,barplot"/> <output name="log" file="log.txt" /> <output_collection name="text_output"> - <element name="cluster_profiler_GGO_CC.csv" file="cluster_profiler_GGO_CC.csv" ftype="csv"/> - <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_GGO_BP.csv" ftype="csv"/> - <element name="cluster_profiler_GGO_MF.csv" file="cluster_profiler_GGO_MF.csv" ftype="csv"/> - <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/> - <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/> - <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/> + <element name="cluster_profiler_GGO_CC.tsv" file="cluster_profiler_GGO_CC.csv" ftype="tsv"/> +<!--- <element name="cluster_profiler_GGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/> --> + <element name="cluster_profiler_GGO_MF.tsv" file="cluster_profiler_GGO_MF.csv" ftype="tsv"/> + <element name="cluster_profiler_EGO_CC.tsv" file="cluster_profiler_EGO_CC.csv" ftype="tsv"/> + <element name="cluster_profiler_EGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/> + <element name="cluster_profiler_EGO_MF.tsv" file="cluster_profiler_EGO_MF.csv" ftype="tsv"/> </output_collection> <output_collection name="graph_output"> <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/> @@ -289,11 +290,11 @@ Bioconductor Packages used: - - bioconductor-org.hs.eg.db v3.8.2 - - bioconductor-org.mm.eg.db v3.8.2 - - bioconductor-org.rn.eg.db v3.8.2 - - dose v3.10.2 - - clusterprofiler v 3.12.0 + - bioconductor-org.hs.eg.db v3.12.0 + - bioconductor-org.mm.eg.db v3.12.0 + - bioconductor-org.rn.eg.db v3.12.0 + - dose v3.16.0 + - clusterprofiler v 3.18.1 .. class:: infomark @@ -301,7 +302,7 @@ Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR -Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR +Christophe Caron, Valentin Loux - INRAE, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR This work has been partially funded through the French National Agency for Research (ANR) IFB project.