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comparison goprofiles.xml @ 11:3ddc1f78773d draft

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date Fri, 28 Jun 2019 05:11:15 -0400
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1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.02.27.1"> 1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.06.27">
2 <description>(Human, Mouse) [goProfiles]</description> 2 <description>(Human, Mouse) [goProfiles]</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>
68 <option value="Entrez">Entrez Gene ID</option> 68 <option value="Entrez">Entrez Gene ID</option>
69 <option value="UniProt">Uniprot Accession number</option> 69 <option value="UniProt">Uniprot Accession number</option>
70 </param> 70 </param>
71 </when> 71 </when>
72 </conditional> 72 </conditional>
73 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" /> 73 <param name="duplicate" type="boolean" checked="true" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
74 <param name="species" type="select" label="Species"> 74 <param name="species" type="select" label="Species">
75 <option value="org.Hs.eg.db">Human (Homo sapiens)</option> 75 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
76 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option> 76 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
77 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option--> 77 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option-->
78 </param> 78 </param>
144 </tests> 144 </tests>
145 <help><![CDATA[ 145 <help><![CDATA[
146 146
147 **Description** 147 **Description**
148 148
149 This tool is based on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the 149 This tool relies on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
150 number of identifiers having a hit in each category of this level. 150 number of identifiers having a hit in each category of this level.
151 151
152 ----- 152 -----
153 153
154 **Input** 154 **Input**
155 155
156 Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers). 156 Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
157 Only entrez gene ID (e.g : 4151) 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. 157 Only entrez gene ID (e.g. 4151) 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.
158
159 .. class:: warningmark
160
161 In copy/paste mode, the number of IDs considered in input is limited to 5000.
158 162
159 ----- 163 -----
160 164
161 **Parameters** 165 **Parameters**
162 166
170 174
171 **Ouput** 175 **Ouput**
172 176
173 Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category. 177 Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category.
174 178
175 text output: 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) 179 Text output: 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)
176 180
177 ----- 181 -----
178 182
179 .. class:: infomark 183 .. class:: infomark
180 184
185 Packages used:
186 - bioconductor-org.hs.eg.db v3.5.0
187 - bioconductor-org.mm.eg.db v3.5.0
188 - bioconductor-annotationdbi v1.40.0
189 - bioconductor-biobase v2.98.0
190 - goprofiles v1.38.0
191
192 -----
193
194 .. class:: infomark
195
181 **Authors** 196 **Authors**
182 197
183 Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355 198 Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355
184 199
185 ----- 200 -----
186 201
187 .. class:: infomark 202 .. class:: infomark
188 203
189 **Galaxy integration** 204 **Galaxy integration**
190 205
191 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 206 D. Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
192 207
193 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, FR 208 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, FR
194 209
195 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 210 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
196 211
197 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 212 Help: contact@proteore.org for any questions or concerns about this tool.
198
199 ]]></help> 213 ]]></help>
200 <citations> 214 <citations>
201 </citations> 215 </citations>
202 </tool> 216 </tool>