Mercurial > repos > proteore > proteore_topgo

comparison topGO.xml @ 8:ddaa0c318d65 draft

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planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
author proteore
date Fri, 23 Mar 2018 10:43:32 -0400
parents 1b2b81169c66
children 70c0c8757f5f
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7:1b2b81169c66 8:ddaa0c318d65
54 ]]></command> 54 ]]></command>
55 55
56 <inputs> 56 <inputs>
57 <conditional name="inputtype"> 57 <conditional name="inputtype">
58 <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool."> 58 <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool.">
59 <option value="file_all">Input file containing your identifiers</option> 59 <option value="file_all" selected="true">Input file containing your identifiers</option>
60 <option value="copy_paste">Copy/paste your list of IDs</option> 60 <option value="copy_paste">Copy/paste your list of IDs</option>
61 </param> 61 </param>
62 <when value="copy_paste"> 62 <when value="copy_paste">
63 <param name="genelist" type="text" label="Enter a list of identifiers"/> 63 <param name="genelist" type="text" label="Enter a list of identifiers">
64 <sanitizer>
65 <valid initial="string.printable">
66 <remove value="&apos;"/>
67 </valid>
68 <mapping initial="none">
69 <add source="&apos;" target="__sq__"/>
70 </mapping>
71 </sanitizer>
72 </param>
64 </when> 73 </when>
65 <when value="file_all"> 74 <when value="file_all">
66 <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/> 75 <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
67 <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/> 76 <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/>
68 77
214 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf 223 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
215 224
216 **Multiple testing corrections** 225 **Multiple testing corrections**
217 226
218 Furthermore, the following corrections for multiple testing can also be applied : 227 Furthermore, the following corrections for multiple testing can also be applied :
228
219 - holm 229 - holm
230
220 - hochberg 231 - hochberg
232
221 - hommel 233 - hommel
234
222 - bonferroni 235 - bonferroni
236
223 - BH 237 - BH
238
224 - BY 239 - BY
240
225 - fdr 241 - fdr
242
243 -----
244
245 .. class:: infomark
226 246
227 **Authors** 247 **Authors**
228 248
229 Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.30.0. 249 Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.30.0.
230 250