Mercurial > repos > proteore > proteore_clusterprofiler

comparison cluster_profiler.xml @ 7:4609346d8108 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
author proteore
date Tue, 18 Dec 2018 09:21:32 -0500
parents 5e16cec55146
children b29255864039
comparison
equal deleted inserted replaced
6:5e16cec55146 7:4609346d8108
1 <tool id="cluter_profiler" name="clusterProfiler" version="0.1.0"> 1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.18">
2 <description> 2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
3 GO terms classification and enrichment analysis
4 </description>
5 <requirements> 3 <requirements>
6 <requirement type="package" version="3.4.1">R</requirement> 4 <requirement type="package" version="3.4.1">R</requirement>
7 <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>
8 <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>
7 <requirement type="package" version="3.5.0">bioconductor-org.Rn.eg.db</requirement>
9 <requirement type="package" version="3.2.0">bioconductor-dose</requirement> 8 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
10 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement> 9 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
11 </requirements> 10 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
13 Rscript "$__tool_directory__/GO-enrich.R" 12 Rscript "$__tool_directory__/GO-enrich.R"
35 #if $ego.go_enrich == "true" 34 #if $ego.go_enrich == "true"
36 --go_enrich="true" 35 --go_enrich="true"
37 --pval_cutoff="$ego.pval" 36 --pval_cutoff="$ego.pval"
38 --qval_cutoff="$ego.qval" 37 --qval_cutoff="$ego.qval"
39 #if $ego.universe.universe_option == "true" 38 #if $ego.universe.universe_option == "true"
40 #if $ego.universe.universe_input.universe_ids == "text" 39 #if $ego.universe.universe_input.universe_ids == "text"
41 --universe_type="text" 40 --universe_type="text"
42 --universe="$ego.universe.universe_input.txt" 41 --universe="$ego.universe.universe_input.txt"
43 #else 42 #else
44 --universe_type="file" 43 --universe_type="file"
45 --universe="$ego.universe.universe_input.file" 44 --universe="$ego.universe.universe_input.file"
46 --uncol="$ego.universe.universe_input.ncol" 45 --uncol="$ego.universe.universe_input.ncol"
47 --uheader="$ego.universe.universe_input.header" 46 --uheader="$ego.universe.universe_input.header"
47 #end if
48 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
48 #end if 49 #end if
49 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
50 #end if
51 #else 50 #else
52 --go_enrich="false" 51 --go_enrich="false"
53 #end if 52 #end if
54 53
55 --onto_opt="$ontology" 54 --plot="$ego.plot"
56 55 --onto_opt="$ontology" > $log
57 --text_output="$text_output"
58 ]]></command> 56 ]]></command>
59 <inputs> 57 <inputs>
60 <conditional name="input" > 58 <conditional name="input" >
61 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > 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)" >
62 <option value="text">Copy/paste your identifiers</option> 60 <option value="text">Copy/paste your IDs</option>
63 <option value="file" selected="true">Input file containing your identifiers</option> 61 <option value="file" selected="true">Input file containing your IDs</option>
64 </param> 62 </param>
65 <when value="text" > 63 <when value="text" >
66 <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' >
67 <sanitizer> 65 <sanitizer>
68 <valid initial="string.printable"> 66 <valid initial="string.printable">
74 </sanitizer> 72 </sanitizer>
75 </param> 73 </param>
76 </when> 74 </when>
77 <when value="file" > 75 <when value="file" >
78 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> 76 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
79 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 77 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
80 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 78 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
81 </when> 79 </when>
82 </conditional> 80 </conditional>
83 <conditional name="idti" > 81 <conditional name="idti" >
84 <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" > 82 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
85 <option value="Uniprot">UniProt accession number</option> 83 <option value="Uniprot">UniProt accession number (e.g.:P31946)</option>
86 <option value="Entrez">Entrez Gene ID</option> 84 <option value="Entrez">Entrez Gene ID (e.g.:4151)</option>
87 </param> 85 </param>
88 <when value="Uniprot"/> 86 <when value="Uniprot"/>
89 <when value="Entrez"/> 87 <when value="Entrez"/>
90 </conditional> 88 </conditional>
91 89 <param name="species" type="select" label="Species" >
92 <param name="species" type="select" label="Select a species" > 90 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
93 <option value="human">Human</option> 91 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
94 <option value="mouse">Mouse</option> 92 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
95 <option value="rat">Rat</option> 93 </param>
94 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" >
95 <option value="CC">Cellular Component</option>
96 <option value="BP">Biological Process</option>
97 <option value="MF">Molecular Function</option>
96 </param> 98 </param>
97 <conditional name="ggo"> 99 <conditional name="ggo">
98 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/> 100 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/>
99 <when value="true"> 101 <when value="true">
100 <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)"> 102 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level)">
101 <option value="1">1</option> 103 <option value="1">1</option>
102 <option value="2">2</option> 104 <option value="2" selected="True">2</option>
103 <option value="3" selected="True">3</option> 105 <option value="3">3</option>
104 </param> 106 </param>
105 </when> 107 </when>
106 <when value="false"/> 108 <when value="false"/>
107 </conditional> 109 </conditional>
108 <conditional name="ego"> 110 <conditional name="ego">
109 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories enrichment analysis?"/> 111 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories enrichment analysis?"/>
110 <when value="true"> 112 <when value="true">
111 <param name="pval" type="float" value="0.01" label="P-value cut off"/> 113 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
112 <param name="qval" type="float" value="0.05" label="Q-value cut off"/> 114 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
113 <conditional name="universe" > 115 <conditional name="universe" >
114 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs?"/> 116 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs?"/>
115 <when value="true"> 117 <when value="true">
116 <conditional name="universe_input"> 118 <conditional name="universe_input">
117 <param name="universe_ids" type="select" label="Provide your background IDs list" help="Copy/paste or ID list from a file (e.g. table)" > 119 <param name="universe_ids" type="select" label="Enter your background IDs (UniProt Accession number or Entrez Gene ID)" help="Copy/paste or from a file (e.g. table)" >
118 <option value="text">Copy/paste your background identifiers</option> 120 <option value="text">Copy/paste your background IDs</option>
119 <option value="file" selected="true">Input file containing your background identifiers</option> 121 <option value="file" selected="true">Input file containing your background IDs</option>
120 </param> 122 </param>
121 <when value="text" > 123 <when value="text" >
122 <param name="txt" type="text" label="Copy/paste your background identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > 124 <param name="txt" type="text" label="Copy/paste your background IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
123 <sanitizer> 125 <sanitizer>
124 <valid initial="string.printable"> 126 <valid initial="string.printable">
125 <remove value="&apos;"/> 127 <remove value="&apos;"/>
126 </valid> 128 </valid>
127 <mapping initial="none"> 129 <mapping initial="none">
129 </mapping> 131 </mapping>
130 </sanitizer> 132 </sanitizer>
131 </param> 133 </param>
132 </when> 134 </when>
133 <when value="file" > 135 <when value="file" >
134 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your background IDs list" help="" /> 136 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" />
135 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 137 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
136 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 138 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
137 </when> 139 </when>
138 </conditional> 140 </conditional>
139 <conditional name="universe_idti" > 141 <conditional name="universe_idti" >
140 <param name="universe_idtypein" type="select" label="Select type/source of background identifier of your list" help="Please see example of IDs in help section" > 142 <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" >
141 <option value="Uniprot">UniProt accession number</option> 143 <option value="Uniprot">UniProt Accession number</option>
142 <option value="Entrez">Entrez Gene ID</option> 144 <option value="Entrez">Entrez Gene ID</option>
143 </param> 145 </param>
144 <when value="Uniprot"/> 146 <when value="Uniprot"/>
145 <when value="Entrez"/> 147 <when value="Entrez"/>
146 </conditional> 148 </conditional>
147 </when> 149 </when>
148 <when value="false"/> 150 <when value="false"/>
149 </conditional> 151 </conditional>
152 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
153 <option selected = "true" value="dotplot">dot-plot</option>
154 <option value="barplot">bar-plot</option>
155 </param>
150 </when> 156 </when>
151 <when value="false"/> 157 <when value="false"/>
152 </conditional> 158 </conditional>
153
154 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
155 <option value="CC">Cellular Component</option>
156 <option value="BP">Biological Process</option>
157 <option value="MF">Molecular Function</option>
158 </param>
159
160
161
162 </inputs> 159 </inputs>
163 <outputs> 160 <outputs>
164 <data name="text_output" format="tabular" label="clusterProfiler text output" /> 161 <data name="log" format="tsv" label="Cluster profiler" />
165 <collection type="list" label="clusterProfiler diagram outputs" name="output" > 162 <collection type="list" label="clusterProfiler text files" name="text_output">
166 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" /> 163 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
167 </collection> 164 </collection>
165 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
166 <discover_datasets pattern="(?P&lt;designation&gt;.+plot)" ext="png" />
167 </collection>
168 </outputs> 168 </outputs>
169 <tests> 169 <tests>
170 <test> 170 <test>
171 <conditional name="input"> 171 <conditional name="input">
172 <param name="ids" value="file"/> 172 <param name="ids" value="file"/>
175 <param name="ncol" value="c1"/> 175 <param name="ncol" value="c1"/>
176 </conditional> 176 </conditional>
177 <conditional name="idti"> 177 <conditional name="idti">
178 <param name="idtypein" value="Uniprot"/> 178 <param name="idtypein" value="Uniprot"/>
179 </conditional> 179 </conditional>
180 <param name="species" value="human"/> 180 <param name="species" value="org.Hs.eg.db"/>
181 <conditional name="ggo"> 181 <conditional name="ggo">
182 <param name="go_represent" value="true"/> 182 <param name="go_represent" value="true"/>
183 <param name="level" value="3"/> 183 <param name="level" value="3"/>
184 </conditional> 184 </conditional>
185 <conditional name="ego"> 185 <conditional name="ego">
186 <param name="go_enrich" value="false"/> 186 <param name="go_enrich" value="true"/>
187 </conditional> 187 <conditional name="universe_input">
188 <param name="ontology" value="CC"/> 188 <param name="universe_ids" value="file"/>
189 <output name="text_output" file="clusterProfiler_text_output.tabular"/> 189 <param name="file" value="background_ids.txt"/>
190 <output_collection name="output"> 190 <param name="header" value="true"/>
191 <element name="clusterProfiler_diagram_outputs__GGO.CC.png" file="clusterProfiler_diagram_outputs__GGO.CC.png" ftype="png"/> 191 <param name="ncol" value="c7"/>
192 </conditional>
193 <conditional name="universe_idti" >
194 <param name="universe_idtypein" value="Uniprot"/>
195 </conditional>
196 </conditional>
197 <param name="ontology" value="CC,BP,MF"/>
198 <param name="plot" value="dotplot,barplot"/>
199 <output name="log" file="log.txt" />
200 <output_collection name="text_output">
201 <element name="cluster_profiler_GGO_CC.csv" file="cluster_profiler_GGO_CC.csv" ftype="csv"/>
202 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_GGO_BP.csv" ftype="csv"/>
203 <element name="cluster_profiler_GGO_MF.csv" file="cluster_profiler_GGO_MF.csv" ftype="csv"/>
204 <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/>
205 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/>
206 <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/>
207 </output_collection>
208 <output_collection name="graph_output">
209 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
210 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
211 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
212 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
213 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
214 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
215 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
192 </output_collection> 216 </output_collection>
193 </test> 217 </test>
194 </tests> 218 </tests>
195 <help><![CDATA[ 219 <help><![CDATA[
196 220
197 **Galaxy component based on R package clusterProfiler (see ref below)** 221 **Description**
198 222
199 This component allows to perform GO enrichment-analyses. 223 This tool is based on R package clusterProfiler and allows to perform GO terms classification and enrichment analyses on gene/protein sets (e.g. given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene/protein set).
200 224
201 Given a list of IDs, the tool either 225 Given a list of IDs, this tool:
202 (i) performs gene classification based on GO distribution at a specific level, or 226
203 (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). 227 (i) performs gene classification based on GO distribution at a specific level,
204 228
205 **Input required** 229 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background. User has the possibility to use background corresponding to the whole organism or to a user-defined list. In this latter case, we recommand to use the "Build tissue-specific expression dataset" ProteoRE tool to create this list according to your need.
206 230
207 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 231 -----
208 232
209 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) 233 **Input**
210 or by copy/pasting your IDs (separated by a space). 234
211 235 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).
212 236
237 "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.
238
239 -----
240
241 **Parameters**
242
243 "Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus
244
245 "Perform GO categories representation analysis?": classify genes based on their projection at a specific level of the GO corpus (see parameter below), and provides functions (set to "Yes")
246
247 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 3) (set to level "2" by default). In general the higher the level, the more semantically specific the term is.
248
249 "Perform GO categories enrichment analysis?": calculate enrichment test for GO terms based on hypergeometric distribution (set to "Yes")
250
251 "P-value cut off": P-value threshold value for the declaration of significance (default is < 0.01)
252
253 "Q-value cut off": to prevent high false discovery rate (FDR) in multiple testing, Q-values (adjusted P-values) are estimated for FDR control. (default is < 0.05)
254
255 "Define your own background IDs?": by default the whole genome/proteome is used as a reference background to compute the enrichment. As this reference set should normally only include genes/proteins that were monitored during your analysis, this option allows to provide your own background; this could be for instance, the total number of genes/proteins expressed in the tissue/sample under study.
256
257 If you want to use your own background, click on the "Yes" button. Your gene/protein set must be a list of Entrez gene ID or Uniprot accession number (otherwise, use the ID-Converter tool of ProteoRE). Select the file containing your list of ID (as background), then specify the column number which contains IDs and the type of IDs (gene Entrez or Uniprot Accession number) as requested.
258
259 Of note: for Human species, you can build your own background by using the "Build tissue-specific expression dataset" tool of ProteoRE.
260
261 -----
262
213 **Output** 263 **Output**
214 264
215 Text (tables) and graphics representing the repartition and/or enrichment of GO categories. 265 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
216 266 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.
217 **User manual / Documentation** of the clusterProfiler R package (functions and parameters): 267
268 -----
269
270 **Authors**
271 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
272 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)
273
274 User manual / Documentation of the clusterProfiler R package (functions and parameters):
218 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html 275 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
219 (Very well explained)
220
221 **Reference**
222
223 clusterProfiler R package reference :
224 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
225 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
226 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
227 276
228 ----- 277 -----
229 278
230 .. class:: infomark 279 .. class:: infomark
231 280
232 **Galaxy integration** 281 **Galaxy integration**
233 282
234 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 283 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
235 284
236 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 285 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
237 286
238 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 287 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
239 288
240 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 289 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
241 290