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comparison topGO.xml @ 12:8eaa43ba1bfc draft

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author proteore
date Fri, 28 Jun 2019 05:18:20 -0400
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1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.02.19"> 1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.27">
2 <description>(Human, Mouse, Rat)[topGO]</description> 2 <description>(Human, Mouse, Rat)[topGO]</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="3.0.0">r-ggplot2</requirement> 5 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> 6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
49 49
50 ]]></command> 50 ]]></command>
51 51
52 <inputs> 52 <inputs>
53 <conditional name="inputtype"> 53 <conditional name="inputtype">
54 <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene only)" help="Copy/paste or from a file"> 54 <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene Id)" help="Copy/paste or from a file">
55 <option value="file" selected="true">Input file containing your IDs</option> 55 <option value="file" selected="true">Input file containing your IDs</option>
56 <option value="copy_paste">Copy/paste your list of IDs</option> 56 <option value="copy_paste">Copy/paste your list of IDs</option>
57 </param> 57 </param>
58 <when value="copy_paste"> 58 <when value="copy_paste">
59 <param name="genelist" type="text" label="Enter a list of IDs"> 59 <param name="genelist" type="text" label="Enter a list of IDs">
74 </param> 74 </param>
75 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 75 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
76 </when> 76 </when>
77 </conditional> 77 </conditional>
78 <conditional name="background_genes"> 78 <conditional name="background_genes">
79 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/> 79 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Use your own background (ID list) ?"/>
80 <when value="true"> 80 <when value="true">
81 <conditional name="inputtype"> 81 <conditional name="inputtype">
82 <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)"> 82 <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)">
83 <option value="file" selected="true">Input file containing your background IDs</option> 83 <option value="file" selected="true">Input file containing your background IDs</option>
84 <option value="copy_paste">Copy/paste your background IDs</option> 84 <option value="copy_paste">Copy/paste your background IDs</option>
104 </when> 104 </when>
105 </conditional> 105 </conditional>
106 </when> 106 </when>
107 <when value="false"/> 107 <when value="false"/>
108 </conditional> 108 </conditional>
109 <param name="geneuniverse" type="select" label="Species"> 109 <param name="geneuniverse" type="select" label="Species (human, mouse, rat)">
110 <!--option value="org.At.tair.db" >Arabidopsis</option--> 110 <!--option value="org.At.tair.db" >Arabidopsis</option-->
111 <!--option value="org.Ce.eg.db" >Worm (C. elegans)</option--> 111 <!--option value="org.Ce.eg.db" >Worm (C. elegans)</option-->
112 <!--option value="org.Dm.eg.db" >Fly (D. melanogaster)</option--> 112 <!--option value="org.Dm.eg.db" >Fly (D. melanogaster)</option-->
113 <option value="org.Hs.eg.db" selected="true">Human (Homo sapiens)</option> 113 <option value="org.Hs.eg.db" selected="true">Human (Homo sapiens)</option>
114 <option value="org.Mm.eg.db" >Mouse (Mouse musculus)</option> 114 <option value="org.Mm.eg.db" >Mouse (Mouse musculus)</option>
118 <param name="ontocat" type="select" label="GO terms category"> 118 <param name="ontocat" type="select" label="GO terms category">
119 <option value="BP" >Biological Process</option> 119 <option value="BP" >Biological Process</option>
120 <option value="CC" >Cellular Component</option> 120 <option value="CC" >Cellular Component</option>
121 <option value="MF" >Molecular Function</option> 121 <option value="MF" >Molecular Function</option>
122 </param> 122 </param>
123 <param name="option" type="select" label="Select the topGO parameter (see user doc)"> 123 <param name="option" type="select" label="Select GO scoring method (read user doc section)">
124 <option value="classic" >Classic Fisher test</option> 124 <option value="classic" >Classic Fisher test</option>
125 <option value="elim" selected="true">Elim</option> 125 <option value="elim" selected="true">Elim</option>
126 <option value="weight01" >Weight01</option> 126 <option value="weight01" >Weight01</option>
127 <option value="parentchild" >ParentChild</option> 127 <option value="parentchild" >ParentChild</option>
128 </param> 128 </param>
168 </conditional> 168 </conditional>
169 <param name="ontocat" value="BP"/> 169 <param name="ontocat" value="BP"/>
170 <param name="option" value="elim"/> 170 <param name="option" value="elim"/>
171 <param name="threshold" value="1e-3"/> 171 <param name="threshold" value="1e-3"/>
172 <param name="correction" value="BH"/> 172 <param name="correction" value="BH"/>
173 <conditional name="condtext"> 173 <param name="textoutput" value="TRUE"/>
174 <param name="textoutput" value="TRUE"/> 174 <param name="plot" value="dotplot,barplot"/>
175 </conditional>
176 <conditional name="condbar">
177 <param name="barplotoutput" value="TRUE"/>
178 </conditional>
179 <conditional name="conddot">
180 <param name="dotoutput" value="TRUE"/>
181 </conditional>
182 <param name="geneuniverse" value="org.Hs.eg.db"/> 175 <param name="geneuniverse" value="org.Hs.eg.db"/>
183 <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/> 176 <output name="outputtext" file="result.tsv"/>
184 <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/> 177 <output name="outputbarplot" file="barplot.png" compare="sim_size"/>
185 <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/> 178 <output name="outputdotplot" file="dotplot.png" compare="sim_size"/>
186 </test> 179 </test>
187 </tests> 180 </tests>
188 <help><![CDATA[ 181 <help><![CDATA[
189 182
190 183
207 200
208 "Species": "Species": the three available species are Homo sapiens, Mus musculus and Rattus norvegicus 201 "Species": "Species": the three available species are Homo sapiens, Mus musculus and Rattus norvegicus
209 202
210 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF) 203 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF)
211 204
212 "Select the topGO parameter (see user doc)": topGO provides a classic Fisher test for evaluating which GO terms are over-represented in your gene/protein list; other methodologies are also provided (Elim, Weight01, Parentchild). For the merits of each option and their algorithmic descriptions, please refer to topGO manual: 205 "Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual:
213 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf 206 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
214 207
215 "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001) 208 "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001)
216 209
217 "Multiple testing procedure (p-value adjustment): several FDR procedure for multiple testing and p-value adjustment are available: Holm, Hochberg 210 "Multiple testing procedure (p-value adjustment): several FDR procedure for multiple testing and p-value adjustment are available: Holm, Hochberg
219 212
220 ----- 213 -----
221 214
222 **Output** 215 **Output**
223 216
224 Three outputs are available : a textual output, a barplot and/or a dotplot (set by default) graphical outputs. 217 Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)).
225 218
226 *Textual output* 219 *Textual output*
227 220
228 The text output lists all the GO-terms that were found significantly enriched according to the specified threshold (p-value). 221 The text output lists all the GO-terms that were found significantly enriched according to the specified threshold (p-value).
229 222
241 234
242 ----- 235 -----
243 236
244 .. class:: infomark 237 .. class:: infomark
245 238
239 Packages used:
240 - bioconductor-org.hs.eg.db v3.5.0
241 - bioconductor-org.mm.eg.db v3.5.0
242 - bioconductor-org.rn.eg.db v3.5.0
243 - bioconductor-annotationdbi v1.40.0
244 - bioconductor-go.db v3.5.0
245 - bioconductor-graph v1.56.0
246 - bioconductor-topgo v2.30.0
247
248 -----
249
250 .. class:: infomark
251
246 **Authors** 252 **Authors**
247 253
248 Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006. 22(13):1600-7. PubMed PMID: 16606683. 254 Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006. 22(13):1600-7. PubMed PMID: 16606683.
249 255
250 ----- 256 -----
251 257
252 .. class:: infomark 258 .. class:: infomark
253 259
254 **Galaxy integration** 260 **Galaxy integration**
255 261
256 Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 262 Lisa Perus, Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
257 263
258 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 264 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
259 265
260 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 266 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
261 267
262 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 268 Help: contact@proteore.org for any questions or concerns about this tool.
263 269
264 ]]></help> 270 ]]></help>
265 <citations> 271 <citations>
266 </citations> 272 </citations>
267 273