Mercurial > repos > proteore > proteore_topgo
comparison topGO.xml @ 9:70c0c8757f5f draft
planemo upload commit 9d3e0b226140b566fc529fd0ffe7aa9e8388c6e5-dirty
| author | proteore |
|---|---|
| date | Fri, 21 Sep 2018 05:32:38 -0400 |
| parents | ddaa0c318d65 |
| children | e3430084c996 |
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| 8:ddaa0c318d65 | 9:70c0c8757f5f |
|---|---|
| 1 <tool id="topGO" name="topGO" version="0.1.0"> | 1 <tool id="topGO" name="topGO" version="2018.09.21"> |
| 2 <description> | 2 <description> |
| 3 Enrichment analysis for Gene Ontology | 3 Enrichment analysis for Gene Ontology |
| 4 </description> | 4 </description> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="3.4.1">R</requirement> | 6 <requirement type="package" version="3.4.1">R</requirement> |
| 7 <requirement type="package" version="2.2.1">r-ggplot2</requirement> | 7 <requirement type="package" version="3.0.0">r-ggplot2</requirement> |
| 8 <requirement type="package" version="3.4.1">bioconductor-org.hs.eg.db</requirement> | 8 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> |
| 9 <requirement type="package" version="1.54.0">bioconductor-graph</requirement> | 9 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> |
| 10 <requirement type="package" version="1.38.2">bioconductor-annotationdbi</requirement> | 10 <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement> |
| 11 <requirement type="package" version="3.4.1">bioconductor-go.db</requirement> | 11 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> |
| 12 <requirement type="package" version="2.28.0">bioconductor-topgo</requirement> | 12 <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement> |
| 13 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement--> | |
| 14 <requirement type="package" version="1.56.0">bioconductor-graph</requirement> | |
| 15 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> | |
| 16 <requirement type="package" version="3.5.0">bioconductor-go.db</requirement> | |
| 17 <requirement type="package" version="2.30.0">bioconductor-topgo</requirement> | |
| 13 </requirements> | 18 </requirements> |
| 14 <stdio> | 19 <stdio> |
| 15 <exit_code range="1:" /> | 20 <exit_code range="1:" /> |
| 16 </stdio> | 21 </stdio> |
| 17 <command><![CDATA[ | 22 <command><![CDATA[ |
| 71 </sanitizer> | 76 </sanitizer> |
| 72 </param> | 77 </param> |
| 73 </when> | 78 </when> |
| 74 <when value="file_all"> | 79 <when value="file_all"> |
| 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."/> | 80 <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."/> |
| 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"/> | 81 <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/> |
| 77 | 82 |
| 78 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> | 83 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> |
| 79 <option value="TRUE" selected="true">Yes</option> | 84 <option value="TRUE" selected="true">Yes</option> |
| 80 <option value="FALSE" selected="false">No</option> | 85 <option value="FALSE" selected="false">No</option> |
| 81 </param> | 86 </param> |
| 82 </when> | 87 </when> |
| 83 </conditional> | 88 </conditional> |
| 84 <param name="geneuniverse" type="select" label="Select a specie"> | 89 <param name="geneuniverse" type="select" label="Select a specie"> |
| 85 <option value="org.At.tair.db" >Arabidopsis</option> | 90 <!--option value="org.At.tair.db" >Arabidopsis</option--> |
| 86 <option value="org.Ce.eg.db" >C.elegans</option> | 91 <option value="org.Ce.eg.db" >Worm (C. elegans)</option> |
| 87 <option value="org.Dm.eg.db" >Fly</option> | 92 <option value="org.Dm.eg.db" >Fly (D. melanogaster)</option> |
| 88 <option value="org.Hs.eg.db" selected="true">Human</option> | 93 <option value="org.Hs.eg.db" selected="true">Human (H. sapiens)</option> |
| 89 <option value="org.Mm.eg.db" >Mouse</option> | 94 <option value="org.Mm.eg.db" >Mouse (M. musculus)</option> |
| 90 <option value="org.Sc.sqd.db" >Yeast</option> | 95 <option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option> |
| 91 </param> | 96 </param> |
| 92 | 97 |
| 93 <param name="ontocat" type="select" label="Ontology category"> | 98 <param name="ontocat" type="select" label="Ontology category"> |
| 94 <option value="BP" >Biological Process</option> | 99 <option value="BP" >Biological Process</option> |
| 95 <option value="CC" >Cellular Component</option> | 100 <option value="CC" >Cellular Component</option> |