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comparison cluster_profiler.xml @ 5:8a91f58782df draft

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author proteore
date Fri, 23 Mar 2018 10:01:41 -0400
parents 710414ebb6db
children 5e16cec55146
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46 ]]></command> 46 ]]></command>
47 <inputs> 47 <inputs>
48 <conditional name="input" > 48 <conditional name="input" >
49 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > 49 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
50 <option value="text">Copy/paste your identifiers</option> 50 <option value="text">Copy/paste your identifiers</option>
51 <option value="file">Input file containing your identifiers</option> 51 <option value="file" selected="true">Input file containing your identifiers</option>
52 </param> 52 </param>
53 <when value="text" > 53 <when value="text" >
54 <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' > 54 <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' >
55 <sanitizer> 55 <sanitizer>
56 <valid initial="string.printable"> 56 <valid initial="string.printable">
98 <param name="pval" type="float" value="0.01" label="P-value cut off"/> 98 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
99 <param name="qval" type="float" value="0.05" label="Q-value cut off"/> 99 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
100 </when> 100 </when>
101 <when value="false"/> 101 <when value="false"/>
102 </conditional> 102 </conditional>
103 <!--conditional name="fun" >
104 <param name="go_function" type="select" display="checkboxes" multiple="true" label="Please select analyses to perform">
105 <option value="ggo">GO categories representation</option>
106 <option value="ego">GO categories enrichment (compared to a background/reference)</option>
107 </param>
108 <when value="ggo" >
109 <param name="level" type="select" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)">
110 <option value="1">1</option>
111 <option value="2">2</option>
112 <option value="3" selected="True">3</option>
113 </param>
114 </when>
115 <when value="ego" >
116 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
117 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
118 </when>
119 </conditional-->
120 103
121 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category"> 104 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
122 <option value="CC">Cellular Component</option> 105 <option value="CC">Cellular Component</option>
123 <option value="BP">Biological Process</option> 106 <option value="BP">Biological Process</option>
124 <option value="MF">Molecular Function</option> 107 <option value="MF">Molecular Function</option>
159 </output_collection> 142 </output_collection>
160 </test> 143 </test>
161 </tests> 144 </tests>
162 <help><![CDATA[ 145 <help><![CDATA[
163 146
164 **Galaxy component based on R package clusterProfiler (see ref below)** 147 **Galaxy component based on R package clusterProfiler (see ref below)**
165 148
166 This component allows to perform GO enrichment-analyses. 149 This component allows to perform GO enrichment-analyses.
167 Given a list of IDs, the tool either
168 (i) performs gene classification based on GO distribution at a specific level, or
169 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list,
170 compared to a background (whole organism or user-defined list).
171 150
172 **Input required** 151 Given a list of IDs, the tool either
152 (i) performs gene classification based on GO distribution at a specific level, or
153 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background (whole organism or user-defined list).
173 154
174 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 155 **Input required**
175 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained. 156
157 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
158
159 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers)
160 or by copy/pasting your IDs (separated by a space).
176 161
177 162
178 **Output** 163 **Output**
179 164
180 Text (tables) and graphics representing the repartition and/or enrichment of GO categories. 165 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
181 166
182 **User manual / Documentation** of the clusterProfiler R package (functions and parameters): 167 **User manual / Documentation** of the clusterProfiler R package (functions and parameters):
183 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html 168 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
184 (Very well explained) 169 (Very well explained)
185 170
186 **Reference** 171 **Reference**
187 172
188 clusterProfiler R package reference : 173 clusterProfiler R package reference :
189 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. 174 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
190 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. 175 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
191 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118) 176 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
192 177
193 178 -----
194 **Galaxy integration**
195 179
196 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 180 .. class:: infomark
197 181
198 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 182 **Galaxy integration**
199 183
200 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 184 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
201 185
202 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 186 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
187
188 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
189
190 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
203 191
204 192
205 ]]></help> 193 ]]></help>
206 <citations> 194 <citations>
207 </citations> 195 </citations>