Mercurial > repos > proteore > proteore_clusterprofiler

comparison cluster_profiler.xml @ 42:3a990910e7f4 draft default tip

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"planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty"
author proteore
date Fri, 09 Apr 2021 14:38:05 +0000
parents 3fd1ccc57a6a
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41:3fd1ccc57a6a 42:3a990910e7f4
1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.12.06"> 1 <tool id="cluter_profiler" name="Classification and enrichment analysis" version="2021.04.08">
2 <description>(Human, Mouse, Rat)[clusterProfiler]</description> 2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">R</requirement> 4 <requirement type="package" version="4.0.3">r-base</requirement>
5 <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> 5 <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement>
6 <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> 6 <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement>
7 <requirement type="package" version="3.8.2">bioconductor-org.Rn.eg.db</requirement> 7 <requirement type="package" version="3.12.0">bioconductor-org.rn.eg.db</requirement>
8 <requirement type="package" version="3.10.2">bioconductor-dose</requirement> 8 <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement>
9 <requirement type="package" version="3.12.0">bioconductor-clusterprofiler</requirement> 9 <requirement type="package" version="3.16.0">bioconductor-dose</requirement>
10 <requirement type="package" version="3.18.1">bioconductor-clusterprofiler</requirement>
10 </requirements> 11 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
12 Rscript "$__tool_directory__/GO-enrich.R" 13 Rscript "$__tool_directory__/GO-enrich.R"
13 #if $input.ids == "text" 14 #if $input.ids == "text"
14 --input_type="text" 15 --input_type="text"
200 </conditional> 201 </conditional>
201 <param name="ontology" value="CC,BP,MF"/> 202 <param name="ontology" value="CC,BP,MF"/>
202 <param name="plot" value="dotplot,barplot"/> 203 <param name="plot" value="dotplot,barplot"/>
203 <output name="log" file="log.txt" /> 204 <output name="log" file="log.txt" />
204 <output_collection name="text_output"> 205 <output_collection name="text_output">
205 <element name="cluster_profiler_GGO_CC.csv" file="cluster_profiler_GGO_CC.csv" ftype="csv"/> 206 <element name="cluster_profiler_GGO_CC.tsv" file="cluster_profiler_GGO_CC.csv" ftype="tsv"/>
206 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_GGO_BP.csv" ftype="csv"/> 207 <!--- <element name="cluster_profiler_GGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/> -->
207 <element name="cluster_profiler_GGO_MF.csv" file="cluster_profiler_GGO_MF.csv" ftype="csv"/> 208 <element name="cluster_profiler_GGO_MF.tsv" file="cluster_profiler_GGO_MF.csv" ftype="tsv"/>
208 <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/> 209 <element name="cluster_profiler_EGO_CC.tsv" file="cluster_profiler_EGO_CC.csv" ftype="tsv"/>
209 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/> 210 <element name="cluster_profiler_EGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/>
210 <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/> 211 <element name="cluster_profiler_EGO_MF.tsv" file="cluster_profiler_EGO_MF.csv" ftype="tsv"/>
211 </output_collection> 212 </output_collection>
212 <output_collection name="graph_output"> 213 <output_collection name="graph_output">
213 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/> 214 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
214 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/> 215 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
215 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/> 216 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
287 288
288 .. class:: infomark 289 .. class:: infomark
289 290
290 Bioconductor Packages used: 291 Bioconductor Packages used:
291 292
292 - bioconductor-org.hs.eg.db v3.8.2 293 - bioconductor-org.hs.eg.db v3.12.0
293 - bioconductor-org.mm.eg.db v3.8.2 294 - bioconductor-org.mm.eg.db v3.12.0
294 - bioconductor-org.rn.eg.db v3.8.2 295 - bioconductor-org.rn.eg.db v3.12.0
295 - dose v3.10.2 296 - dose v3.16.0
296 - clusterprofiler v 3.12.0 297 - clusterprofiler v 3.18.1
297 298
298 .. class:: infomark 299 .. class:: infomark
299 300
300 **Galaxy integration** 301 **Galaxy integration**
301 302
302 Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 303 Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
303 304
304 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 305 Christophe Caron, Valentin Loux - INRAE, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
305 306
306 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 307 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
307 308
308 Help: contact@proteore.org for any questions or concerns about this tool. 309 Help: contact@proteore.org for any questions or concerns about this tool.
309 310