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comparison cluster_profiler.xml @ 10:d951677a50d4 draft

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author proteore
date Fri, 28 Jun 2019 05:08:48 -0400
parents 2f67202ffdb3
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9:2f67202ffdb3 10:d951677a50d4
1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.02.18"> 1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.27.1">
2 <description>(Human, Mouse, Rat)[clusterProfiler]</description> 2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.4.1">R</requirement> 4 <requirement type="package" version="3.4.1">R</requirement>
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> 5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> 6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
54 54
55 --onto_opt="$ontology" > $log 55 --onto_opt="$ontology" > $log
56 ]]></command> 56 ]]></command>
57 <inputs> 57 <inputs>
58 <conditional name="input" > 58 <conditional name="input" >
59 <param name="ids" type="select" label="Enter your IDs (UniProt Accession numer or Gene ID)" help="Copy/paste or from a file (e.g. table)" > 59 <param name="ids" type="select" label="Enter your IDs (UniProt Accession number or Gene ID)" help="Copy/paste or from a file (e.g. table)" >
60 <option value="text">Copy/paste your IDs</option> 60 <option value="text">Copy/paste your IDs</option>
61 <option value="file" selected="true">Input file containing your IDs</option> 61 <option value="file" selected="true">Input file containing your IDs</option>
62 </param> 62 </param>
63 <when value="text" > 63 <when value="text" >
64 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > 64 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
80 </param> 80 </param>
81 </when> 81 </when>
82 </conditional> 82 </conditional>
83 <conditional name="idti" > 83 <conditional name="idti" >
84 <param name="idtypein" type="select" label="Select type/source of IDs" help="" > 84 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
85 <option value="Uniprot">UniProt accession number (e.g.:P31946)</option> 85 <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
86 <option value="Entrez">Entrez Gene ID (e.g.:4151)</option> 86 <option value="Entrez">Entrez Gene ID (e.g. 4151)</option>
87 </param> 87 </param>
88 <when value="Uniprot"/> 88 <when value="Uniprot"/>
89 <when value="Entrez"/> 89 <when value="Entrez"/>
90 </conditional> 90 </conditional>
91 <param name="species" type="select" label="Species" > 91 <param name="species" type="select" label="Species" >
99 <option value="MF">Molecular Function</option> 99 <option value="MF">Molecular Function</option>
100 </param> 100 </param>
101 <conditional name="ggo"> 101 <conditional name="ggo">
102 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/> 102 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/>
103 <when value="true"> 103 <when value="true">
104 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level)"> 104 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level, up to 3)">
105 <option value="1">1</option> 105 <option value="1">1</option>
106 <option value="2" selected="True">2</option> 106 <option value="2" selected="True">2</option>
107 <option value="3">3</option> 107 <option value="3">3</option>
108 </param> 108 </param>
109 </when> 109 </when>
141 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> 141 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
142 </param> 142 </param>
143 </when> 143 </when>
144 </conditional> 144 </conditional>
145 <conditional name="universe_idti" > 145 <conditional name="universe_idti" >
146 <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" > 146 <param name="universe_idtypein" type="select" label="Select type of IDs of your background" help="" >
147 <option value="Uniprot">UniProt Accession number</option> 147 <option value="Uniprot">UniProt Accession number</option>
148 <option value="Entrez">Entrez Gene ID</option> 148 <option value="Entrez">Entrez Gene ID</option>
149 </param> 149 </param>
150 <when value="Uniprot"/> 150 <when value="Uniprot"/>
151 <when value="Entrez"/> 151 <when value="Entrez"/>
236 236
237 **Input** 237 **Input**
238 238
239 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space). 239 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space).
240 240
241 "Select type/source of IDs": only entrez gene ID (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE. 241 "Select type/source of IDs": only entrez gene ID (e.g. 4151, 7412) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE.
242
243 .. class:: warningmark
244
245 In copy/paste mode, the number of IDs considered in input is limited to 5000.
242 246
243 ----- 247 -----
244 248
245 **Parameters** 249 **Parameters**
246 250
270 Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)d graphics representing the repartition and/or enrichment of GO categories. One table and one graphic will be produced for each GO catagory. 274 Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)d graphics representing the repartition and/or enrichment of GO categories. One table and one graphic will be produced for each GO catagory.
271 275
272 ----- 276 -----
273 277
274 **Authors** 278 **Authors**
279
275 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. 280 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
276 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118) 281 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
277 282
278 User manual / Documentation of the clusterProfiler R package (functions and parameters): 283 User manual / Documentation of the clusterProfiler R package (functions and parameters):
279 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html 284 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
280 285
281 ----- 286 -----
282 287
283 .. class:: infomark 288 .. class:: infomark
284 289
290 Bioconductor Packages used:
291
292 - bioconductor-org.hs.eg.db v3.5.0
293 - bioconductor-org.mm.eg.db v3.5.0
294 - bioconductor-org.rn.eg.db v3.5.0
295 - dose v3.2.0
296 - clusterprofiler v 3.4.4
297
298 .. class:: infomark
299
285 **Galaxy integration** 300 **Galaxy integration**
286 301
287 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 302 Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
288 303
289 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 304 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
290 305
291 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 306 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
292 307
293 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 308 Help: contact@proteore.org for any questions or concerns about this tool.
294 309
295 310
296 ]]></help> 311 ]]></help>
297 <citations> 312 <citations>
298 </citations> 313 </citations>