Mercurial > repos > proteore > proteore_topgo
comparison topGO.xml @ 12:8eaa43ba1bfc draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author | proteore |
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date | Fri, 28 Jun 2019 05:18:20 -0400 |
parents | fa2e27165d5d |
children | aba2aa04c7aa |
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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 |