Mercurial > repos > iuc > goseq
comparison goseq.xml @ 6:07f6832bdd4d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 11d5198120837fa4eecb0bef8e2c04106eab63c2
| author | iuc |
|---|---|
| date | Sat, 09 Feb 2019 09:07:48 -0500 |
| parents | bbcf5f7f2af2 |
| children | 67c29afac85f |
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| 5:bbcf5f7f2af2 | 6:07f6832bdd4d |
|---|---|
| 1 <tool id="goseq" name="goseq" version="1.32.0"> | 1 <tool id="goseq" name="goseq" version="1.34.0"> |
| 2 <description>tests for overrepresented gene categories</description> | 2 <description>tests for overrepresented gene categories</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.32.0">bioconductor-goseq</requirement> | 4 <requirement type="package" version="1.34.0">bioconductor-goseq</requirement> |
| 5 <requirement type="package" version="3.6.0">bioconductor-org.hs.eg.db</requirement> | 5 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement> |
| 6 <requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement> | 6 <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement> |
| 7 <requirement type="package" version="3.6.0">bioconductor-org.dr.eg.db</requirement> | 7 <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement> |
| 8 <requirement type="package" version="3.6.0">bioconductor-org.mm.eg.db</requirement> | 8 <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement> |
| 9 <requirement type="package" version="0.7.8">r-dplyr</requirement> | 9 <requirement type="package" version="0.7.8">r-dplyr</requirement> |
| 10 <requirement type="package" version="3.1.0">r-ggplot2</requirement> | 10 <requirement type="package" version="3.1.0">r-ggplot2</requirement> |
| 11 <requirement type="package" version="1.6.0">r-optparse</requirement> | 11 <requirement type="package" version="1.6.0">r-optparse</requirement> |
| 12 </requirements> | 12 </requirements> |
| 13 <stdio> | 13 <stdio> |
| 186 <param name="gene_id" value="ensGene" /> | 186 <param name="gene_id" value="ensGene" /> |
| 187 <param name="use_genes_without_cat" value="true" /> | 187 <param name="use_genes_without_cat" value="true" /> |
| 188 <output name="wallenius_tab"> | 188 <output name="wallenius_tab"> |
| 189 <assert_contents> | 189 <assert_contents> |
| 190 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> | 190 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> |
| 191 <has_text_matching expression="GO:0005576.*5.2" /> | 191 <has_text_matching expression="GO:0005576.*8.8" /> |
| 192 </assert_contents> | 192 </assert_contents> |
| 193 </output> | 193 </output> |
| 194 </test> | 194 </test> |
| 195 <!-- Ensure getting GO categories for another genome (zebrafish) works --> | 195 <!-- Ensure getting GO categories for another genome (zebrafish) works --> |
| 196 <test expect_num_outputs="1"> | 196 <test expect_num_outputs="1"> |
| 201 <param name="gene_id" value="ensGene" /> | 201 <param name="gene_id" value="ensGene" /> |
| 202 <param name="use_genes_without_cat" value="true" /> | 202 <param name="use_genes_without_cat" value="true" /> |
| 203 <output name="wallenius_tab"> | 203 <output name="wallenius_tab"> |
| 204 <assert_contents> | 204 <assert_contents> |
| 205 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> | 205 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> |
| 206 <has_text_matching expression="GO:0031324.*0.12" /> | 206 <has_text_matching expression="GO:0031324.*0.50" /> |
| 207 </assert_contents> | 207 </assert_contents> |
| 208 </output> | 208 </output> |
| 209 </test> | 209 </test> |
| 210 <!-- Ensure length bias plot works --> | 210 <!-- Ensure length bias plot works --> |
| 211 <test expect_num_outputs="2"> | 211 <test expect_num_outputs="2"> |