Mercurial > repos > proteore > proteore_topgo
comparison topGO.xml @ 11:fa2e27165d5d draft
planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
| author | proteore |
|---|---|
| date | Mon, 04 Mar 2019 08:37:49 -0500 |
| parents | e3430084c996 |
| children | 8eaa43ba1bfc |
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| 10:e3430084c996 | 11:fa2e27165d5d |
|---|---|
| 1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.12.17"> | 1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.02.19"> |
| 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" version="3.4.1">R</requirement> |
| 5 <requirement type="package" version="3.0.0">r-ggplot2</requirement> | 5 <requirement type="package" version="3.0.0">r-ggplot2</requirement> |
| 6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> | 6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> |
| 67 </sanitizer> | 67 </sanitizer> |
| 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> | |
| 74 </param> | |
| 73 <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?" /> |
| 74 </when> | 76 </when> |
| 75 </conditional> | 77 </conditional> |
| 76 <conditional name="background_genes"> | 78 <conditional name="background_genes"> |
| 77 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/> | 79 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/> |
| 94 </param> | 96 </param> |
| 95 </when> | 97 </when> |
| 96 <when value="file"> | 98 <when value="file"> |
| 97 <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=""/> |
| 98 <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 ?" /> |
| 99 <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> | |
| 103 </param> | |
| 100 </when> | 104 </when> |
| 101 </conditional> | 105 </conditional> |
| 102 </when> | 106 </when> |
| 103 <when value="false"/> | 107 <when value="false"/> |
| 104 </conditional> | 108 </conditional> |
| 139 <option value="barplot">bar-plot</option> | 143 <option value="barplot">bar-plot</option> |
| 140 </param> | 144 </param> |
| 141 </inputs> | 145 </inputs> |
| 142 <outputs> | 146 <outputs> |
| 143 | 147 |
| 144 <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result"> | 148 <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result.tsv"> |
| 145 <filter>textoutput</filter> | 149 <!--filter>textoutput</filter--> |
| 146 </data> | 150 </data> |
| 147 | 151 |
| 152 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png"> | |
| 153 <filter>'dotplot' in plot</filter> | |
| 154 </data> | |
| 155 | |
| 148 <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"> |
| 149 <filter>barplot</filter> | 157 <filter>'barplot' in plot</filter> |
| 150 </data> | |
| 151 | |
| 152 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png"> | |
| 153 <filter>dotplot</filter> | |
| 154 </data> | 158 </data> |
| 155 | 159 |
| 156 </outputs> | 160 </outputs> |
| 157 <tests> | 161 <tests> |
| 158 <test> | 162 <test> |