Mercurial > repos > proteore > proteore_topgo
comparison topGO.xml @ 13:aba2aa04c7aa draft
planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
author | proteore |
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date | Fri, 27 Sep 2019 05:49:07 -0400 |
parents | 8eaa43ba1bfc |
children | 35fc495473ec |
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12:8eaa43ba1bfc | 13:aba2aa04c7aa |
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1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.27"> | 1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.09.26"> |
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">R</requirement> |
5 <requirement type="package" version="3.0.0">r-ggplot2</requirement> | 5 <requirement type="package">r-ggplot2</requirement> |
6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> | 6 <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> |
7 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> | 7 <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> |
8 <requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement> | 8 <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement> |
9 <!--requirement type="package" version="3.6.0">bioconductor-org.ce.eg.db</requirement--> | 9 <!--requirement type="package" version="3.6.0">bioconductor-org.ce.eg.db</requirement--> |
10 <!--requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement--> | 10 <!--requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement--> |
11 <!--requirement type="package" version="3.6.0">bioconductor-org.sc.sgd.db</requirement--> | 11 <!--requirement type="package" version="3.6.0">bioconductor-org.sc.sgd.db</requirement--> |
12 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement--> | 12 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement--> |
13 <requirement type="package" version="1.56.0">bioconductor-graph</requirement> | 13 <requirement type="package" version="1.62.0">bioconductor-graph</requirement> |
14 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> | 14 <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement> |
15 <requirement type="package" version="3.5.0">bioconductor-go.db</requirement> | 15 <requirement type="package" version="3.8.2">bioconductor-go.db</requirement> |
16 <requirement type="package" version="2.30.0">bioconductor-topgo</requirement> | 16 <requirement type="package" version="2.36.0">bioconductor-topgo</requirement> |
17 </requirements> | 17 </requirements> |
18 <stdio> | 18 <stdio> |
19 <exit_code range="1:" /> | 19 <exit_code range="1:" /> |
20 </stdio> | 20 </stdio> |
21 <command><![CDATA[ | 21 <command><![CDATA[ |
22 | 22 |
23 Rscript --vanilla $__tool_directory__/topGO_enrichment.R | 23 Rscript --vanilla $__tool_directory__/topGO_enrichment.R |
24 --inputtype="$inputtype.filetype" | 24 --inputtype="$inputtype.filetype" |
25 --input='$inputtype.genelist' | 25 --input='$inputtype.genelist' |
26 | 26 |
27 #if $inputtype.filetype == "file" | 27 #if $inputtype.filetype == "file" |
28 --column='$inputtype.column' | 28 --column='$inputtype.column' |
33 --option='$option' | 33 --option='$option' |
34 --threshold='$threshold' | 34 --threshold='$threshold' |
35 --correction='$correction' | 35 --correction='$correction' |
36 --textoutput='true' | 36 --textoutput='true' |
37 --plot='$plot' | 37 --plot='$plot' |
38 --geneuniverse='$geneuniverse' | 38 --geneuniverse='$geneuniverse' |
39 --background="$background_genes.background" | 39 --background="$background_genes.background" |
40 | 40 |
41 #if $background_genes.background == "true" | 41 #if $background_genes.background == "true" |
42 --background_genes="$background_genes.inputtype.genelist" | 42 --background_genes="$background_genes.inputtype.genelist" |
43 --background_input_type="$background_genes.inputtype.filetype" | 43 --background_input_type="$background_genes.inputtype.filetype" |
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 Id)" 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"> |
60 <sanitizer> | 60 <sanitizer> |
61 <valid initial="string.printable"> | 61 <valid initial="string.printable"> |
68 </param> | 68 </param> |
69 </when> | 69 </when> |
70 <when value="file"> | 70 <when value="file"> |
71 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> | 71 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> |
72 <param name="column" type="text" 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"> | 72 <param name="column" type="text" 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"> |
73 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | 73 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> |
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="Use your own background (ID list) ?"/> | 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> |
85 </param> | 85 </param> |
86 <when value="copy_paste"> | 86 <when value="copy_paste"> |
87 <param name="genelist" type="text" label="Copy/paste your background IDs" help="IDs must be separated by spaces into the form field, for example: ENSG00000139618 ENSG00000007350"> | 87 <param name="genelist" type="text" label="Copy/paste your background IDs" help="IDs must be separated by spaces into the form field, for example: ENSG00000139618 ENSG00000007350"> |
88 <sanitizer> | 88 <sanitizer> |
89 <valid initial="string.printable"> | 89 <valid initial="string.printable"> |
95 </sanitizer> | 95 </sanitizer> |
96 </param> | 96 </param> |
97 </when> | 97 </when> |
98 <when value="file"> | 98 <when value="file"> |
99 <param name="genelist" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help=""/> | 99 <param name="genelist" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help=""/> |
100 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header ?" /> | 100 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header ?" /> |
101 <param name="column" type="text" label="Column number of IDs" value="c1" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on"> | 101 <param name="column" type="text" label="Column number of IDs" value="c1" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on"> |
102 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | 102 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> |
103 </param> | 103 </param> |
104 </when> | 104 </when> |
105 </conditional> | 105 </conditional> |
106 </when> | 106 </when> |
107 <when value="false"/> | 107 <when value="false"/> |
108 </conditional> | 108 </conditional> |
154 </data> | 154 </data> |
155 | 155 |
156 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png"> | 156 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png"> |
157 <filter>'barplot' in plot</filter> | 157 <filter>'barplot' in plot</filter> |
158 </data> | 158 </data> |
159 | 159 |
160 </outputs> | 160 </outputs> |
161 <tests> | 161 <tests> |
162 <test> | 162 <test> |
163 <conditional name="inputtype"> | 163 <conditional name="inputtype"> |
164 <param name="filetype " value="tabfile"/> | 164 <param name="filetype " value="tabfile"/> |
167 <param name="header" value="TRUE"/> | 167 <param name="header" value="TRUE"/> |
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 <param name="textoutput" value="TRUE"/> | 173 <param name="textoutput" value="TRUE"/> |
174 <param name="plot" value="dotplot,barplot"/> | 174 <param name="plot" value="dotplot,barplot"/> |
175 <param name="geneuniverse" value="org.Hs.eg.db"/> | 175 <param name="geneuniverse" value="org.Hs.eg.db"/> |
176 <output name="outputtext" file="result.tsv"/> | 176 <output name="outputtext" file="result.tsv"/> |
177 <output name="outputbarplot" file="barplot.png" compare="sim_size"/> | 177 <output name="outputbarplot" file="barplot.png" compare="sim_size"/> |
178 <output name="outputdotplot" file="dotplot.png" compare="sim_size"/> | 178 <output name="outputdotplot" file="dotplot.png" compare="sim_size"/> |
179 </test> | 179 </test> |
180 </tests> | 180 </tests> |
181 <help><![CDATA[ | 181 <help><![CDATA[ |
182 | 182 |
183 | 183 |
184 **Description** | 184 **Description** |
185 | 185 |
186 This tool is based on R package topGO. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be applied. | 186 This tool is based on R package topGO. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be applied. |
187 | 187 |
188 This component computes the GO terms representativity of a gene list in one ontology category (Biological Process "BP", Cellular Component "CC", Molecular Function "MF"). This representativity is evaluated in comparison to the background list of all genes/proteins (of the selected species) associated associated with GO terms of the chosen category (BP,CC,MF). | 188 This component computes the GO terms representativity of a gene list in one ontology category (Biological Process "BP", Cellular Component "CC", Molecular Function "MF"). This representativity is evaluated in comparison to the background list of all genes/proteins (of the selected species) associated associated with GO terms of the chosen category (BP,CC,MF). |
190 ----- | 190 ----- |
191 | 191 |
192 **Input required** | 192 **Input required** |
193 | 193 |
194 This component works with Ensembl gene IDs (e.g : ENSG0000013618). You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) | 194 This component works with Ensembl gene IDs (e.g : ENSG0000013618). You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) |
195 and then specifying the column number that contains the ENSG IDs. | 195 and then specifying the column number that contains the ENSG IDs. |
196 | 196 |
197 ----- | 197 ----- |
198 | 198 |
199 **Parameters** | 199 **Parameters** |
200 | 200 |
201 "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 |
202 | 202 |
203 "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) |
204 | 204 |
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: | 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: |
206 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 |
207 | 207 |
208 "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) |
209 | 209 |
210 "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 |
212 | 212 |
213 ----- | 213 ----- |
214 | 214 |
215 **Output** | 215 **Output** |
216 | 216 |
217 Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)). | 217 Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)). |
218 | 218 |
219 *Textual output* | 219 *Textual output* |
220 | 220 |
221 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). |
222 | 222 |
223 The different fields are as follow: | 223 The different fields are as follow: |
224 | 224 |
225 - Annotated : number of genes in the selected species that are annotated with the GO-term. | 225 - Annotated : number of genes in the selected species that are annotated with the GO-term. |
226 | 226 |
227 - Significant : number of genes belonging to your input annotated with the GO-term. | 227 - Significant : number of genes belonging to your input annotated with the GO-term. |
228 | 228 |
229 - Expected : represents the expected number of interesting genes mapped to the GO term if the interesting genes were randomly distributed over all GO terms. | 229 - Expected : represents the expected number of interesting genes mapped to the GO term if the interesting genes were randomly distributed over all GO terms. |
230 | 230 |
231 - p-values : p-value obtained after the test | 231 - p-values : p-value obtained after the test |
232 | 232 |
233 - ( q-values : additional column with adjusted pvalues ) | 233 - ( q-values : additional column with adjusted pvalues ) |
234 | 234 |
235 ----- | 235 ----- |
236 | 236 |
237 .. class:: infomark | 237 .. class:: infomark |
238 | 238 |
239 Packages used: | 239 Packages used: |
240 - bioconductor-org.hs.eg.db v3.5.0 | 240 - bioconductor-org.hs.eg.db v3.8.2 |
241 - bioconductor-org.mm.eg.db v3.5.0 | 241 - bioconductor-org.mm.eg.db v3.8.2 |
242 - bioconductor-org.rn.eg.db v3.5.0 | 242 - bioconductor-org.rn.eg.db v3.8.2 |
243 - bioconductor-annotationdbi v1.40.0 | 243 - bioconductor-annotationdbi v1.46.0 |
244 - bioconductor-go.db v3.5.0 | 244 - bioconductor-go.db v3.8.2 |
245 - bioconductor-graph v1.56.0 | 245 - bioconductor-graph v1.62.0 |
246 - bioconductor-topgo v2.30.0 | 246 - bioconductor-topgo v2.36.0 |
247 | 247 |
248 ----- | 248 ----- |
249 | 249 |
250 .. class:: infomark | 250 .. class:: infomark |
251 | 251 |