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comparison annotateMyIDs.xml @ 8:b5d8e5475247 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit bfab2e2b811849e2c9159e4d14b47a215e4bf990"
author iuc
date Fri, 12 Jun 2020 15:06:01 -0400
parents 1aae04680c4b
children 44018dd6b447
comparison
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7:1aae04680c4b 8:b5d8e5475247
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.7.0+galaxy1"> 1 <tool id="annotatemyids" name="annotateMyIDs" version="3.7.0+galaxy2">
2 <description>annotate a generic set of identifiers</description> 2 <description>annotate a generic set of identifiers</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement> 4 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
5 <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement> 5 <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement>
6 <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement> 6 <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement>
86 <option value="SYMBOL">Gene Symbol</option> 86 <option value="SYMBOL">Gene Symbol</option>
87 <option value="ZFIN">Zfin</option> 87 <option value="ZFIN">Zfin</option>
88 </param> 88 </param>
89 <param name="output_cols" type="select" multiple="True" display="checkboxes" label="Output columns" help="Choose the columns you want in the output table. Note that selecting some columns such as GO or KEGG could make the table very large as some genes may be associated with many terms. Default: ENSEMBL, ENTREZID, SYMBOL, GENENAME"> 89 <param name="output_cols" type="select" multiple="True" display="checkboxes" label="Output columns" help="Choose the columns you want in the output table. Note that selecting some columns such as GO or KEGG could make the table very large as some genes may be associated with many terms. Default: ENSEMBL, ENTREZID, SYMBOL, GENENAME">
90 <option value="ALIAS">ALIAS</option> 90 <option value="ALIAS">ALIAS</option>
91 <option value="DESCRIPTION">DESCRIPTION</option>
92 <option value="ENSEMBL" selected="True">ENSEMBL</option> 91 <option value="ENSEMBL" selected="True">ENSEMBL</option>
93 <option value="ENTREZID" selected="True">ENTREZID</option> 92 <option value="ENTREZID" selected="True">ENTREZID</option>
94 <option value="EVIDENCE">EVIDENCE</option> 93 <option value="EVIDENCE">EVIDENCE</option>
95 <option value="SYMBOL" selected="True">SYMBOL</option> 94 <option value="SYMBOL" selected="True">SYMBOL</option>
96 <option value="GENENAME" selected="True">GENENAME</option> 95 <option value="GENENAME" selected="True">GENENAME</option>
223 =============== ============ ========== ================================= 222 =============== ============ ========== =================================
224 223
225 Columns available for output include many of the ID columns already described under Inputs above and also: 224 Columns available for output include many of the ID columns already described under Inputs above and also:
226 225
227 * **ALIAS**: Commonly used gene symbols 226 * **ALIAS**: Commonly used gene symbols
228 * **DESCRIPTION**: The description of the associated gene
229 * **EVIDENCE**: Evidence codes for GO associations with a gene of interest 227 * **EVIDENCE**: Evidence codes for GO associations with a gene of interest
230 * **GENENAME**: The full gene name 228 * **GENENAME**: The full gene name
231 * **ONTOLOGY**: For GO Identifiers, which Gene Ontology (BP, CC, or MF) 229 * **ONTOLOGY**: For GO Identifiers, which Gene Ontology (BP, CC, or MF)
232 230
233 ]]></help> 231 ]]></help>