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comparison goprofiles.xml @ 12:d4dd1c242a87 draft

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planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72
author proteore
date Fri, 27 Sep 2019 05:48:43 -0400
parents 3ddc1f78773d
children b42399e8d3bf
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11:3ddc1f78773d 12:d4dd1c242a87
1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.06.27"> 1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.09.26">
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" >R</requirement>
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> 5 <requirement type="package" version="3.8.2">-org.hs.eg.db</requirement>
6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> 6 <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
7 <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement--> 7 <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
8 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> 8 <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement>
9 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> 9 <requirement type="package" version="2.44.0">bioconductor-biobase</requirement>
10 <requirement type="package" version="1.38.0">goprofiles</requirement> 10 <requirement type="package" version="1.46.0">bioconductor-goprofiles</requirement>
11 11
12 </requirements> 12 </requirements>
13 <stdio> 13 <stdio>
14 <exit_code range="1:" /> 14 <exit_code range="1:" />
15 </stdio> 15 </stdio>
16 <command><![CDATA[ 16 <command><![CDATA[
22 --input_type="file" 22 --input_type="file"
23 --input="$input.file" 23 --input="$input.file"
24 --ncol="$input.ncol" 24 --ncol="$input.ncol"
25 --header="$input.header" 25 --header="$input.header"
26 #end if 26 #end if
27 27
28 --id_type="$input.id_type" 28 --id_type="$input.id_type"
29 --onto_opt="$onto_opt" 29 --onto_opt="$onto_opt"
30 --plot_opt="$plot_opt" 30 --plot_opt="$plot_opt"
31 --level="$level" 31 --level="$level"
32 --per="$per" 32 --per="$per"
66 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 66 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
67 <param name="id_type" type="select" label="Select type of IDs list" > 67 <param name="id_type" type="select" label="Select type of IDs list" >
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" checked="true" 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>
95 <valid initial="string.printable"> 95 <valid initial="string.printable">
96 <remove value="&apos;"/> 96 <remove value="&apos;"/>
97 <remove value="/"/> 97 <remove value="/"/>
98 </valid> 98 </valid>
99 <mapping> 99 <mapping>
100 <add source="&#x20;" target=""/> 100 <add source="&#x20;" target=""/>
101 </mapping> 101 </mapping>
102 </sanitizer> 102 </sanitizer>
103 </param> 103 </param>
104 <param type="select" name="plot_opt" label="Plot file format"> 104 <param type="select" name="plot_opt" label="Plot file format">
105 <option value="PNG" selected="True">png</option> 105 <option value="PNG" selected="True">png</option>
123 <test> 123 <test>
124 <conditional name="input"> 124 <conditional name="input">
125 <param name="ids" value="file" /> 125 <param name="ids" value="file" />
126 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" /> 126 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
127 <param name="ncol" value="c1" /> 127 <param name="ncol" value="c1" />
128 <param name="header" value="true" /> 128 <param name="header" value="true" />
129 <param name="id_type" value="UniProt" /> 129 <param name="id_type" value="UniProt" />
130 </conditional> 130 </conditional>
131 <param name="duplicate" value="false"/> 131 <param name="duplicate" value="false"/>
132 <param name="onto_opt" value="CC,MF,BP" /> 132 <param name="onto_opt" value="CC,MF,BP" />
133 <param name="level" value="2" /> 133 <param name="level" value="2" />
134 <param name="per" value="true" /> 134 <param name="per" value="true" />
145 <help><![CDATA[ 145 <help><![CDATA[
146 146
147 **Description** 147 **Description**
148 148
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 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.
158 158
159 .. class:: warningmark 159 .. class:: warningmark
160 160
161 In copy/paste mode, the number of IDs considered in input is limited to 5000. 161 In copy/paste mode, the number of IDs considered in input is limited to 5000.
162 162
163 ----- 163 -----
164 164
165 **Parameters** 165 **Parameters**
166 166
167 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon) 167 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)
168 168
169 "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF) 169 "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF)
170 170
171 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is. 171 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is.
172 172
173 ----- 173 -----
174 174
175 **Ouput** 175 **Ouput**
176 176
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. 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.
178 178
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) 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)
180 180
181 ----- 181 -----
182 182
183 .. class:: infomark 183 .. class:: infomark
184 184
185 Packages used: 185 Packages used:
186 - bioconductor-org.hs.eg.db v3.5.0 186 - bioconductor-org.hs.eg.db v3.5.0
187 - bioconductor-org.mm.eg.db v3.5.0 187 - bioconductor-org.mm.eg.db v3.5.0
188 - bioconductor-annotationdbi v1.40.0 188 - bioconductor-annotationdbi v1.40.0
189 - bioconductor-biobase v2.98.0 189 - bioconductor-biobase v2.98.0
190 - goprofiles v1.38.0 190 - goprofiles v1.38.0
191 191
192 ----- 192 -----
193 193
194 .. class:: infomark 194 .. class:: infomark
195 195
196 **Authors** 196 **Authors**
197 197
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 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
199 199
200 ----- 200 -----
201 201