Mercurial > repos > iuc > goseq
comparison goseq.xml @ 9:ef2ad746b589 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e230a8db9e090c6e0ea9577863ec6153df79e145"
author | iuc |
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date | Sun, 06 Jun 2021 22:47:36 +0000 |
parents | 8b3e3657034e |
children | 43798b4caee0 |
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8:8b3e3657034e | 9:ef2ad746b589 |
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1 <tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@"> | 1 <tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@"> |
2 <description>tests for overrepresented gene categories</description> | 2 <description>tests for overrepresented gene categories</description> |
3 <xrefs> | |
4 <xref type="bio.tools">goseq</xref> | |
5 </xrefs> | |
6 <edam_topics> | |
7 <edam_topic>topic_3308</edam_topic> | |
8 </edam_topics> | |
9 <edam_operations> | |
10 <edam_operation>operation_2436</edam_operation> | |
11 </edam_operations> | |
3 <macros> | 12 <macros> |
4 <token name="@VERSION@">1.36.0</token> | 13 <token name="@VERSION@">1.44.0</token> |
5 <token name="@GALAXY_VERSION@">galaxy0</token> | 14 <token name="@GALAXY_VERSION@">galaxy0</token> |
6 </macros> | 15 </macros> |
7 <requirements> | 16 <requirements> |
8 <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement> | 17 <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement> |
9 <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> | 18 <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement> |
10 <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement> | 19 <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement> |
11 <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement> | 20 <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement> |
12 <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> | 21 <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement> |
13 <requirement type="package" version="0.8.3">r-dplyr</requirement> | 22 <requirement type="package" version="1.0.6">r-dplyr</requirement> |
14 <requirement type="package" version="3.2.1">r-ggplot2</requirement> | 23 <requirement type="package" version="3.3.3">r-ggplot2</requirement> |
15 <requirement type="package" version="1.6.2">r-optparse</requirement> | 24 <requirement type="package" version="1.6.6">r-optparse</requirement> |
16 </requirements> | 25 </requirements> |
17 <stdio> | 26 <stdio> |
18 <regex match="Execution halted" | 27 <regex match="Execution halted" |
19 source="both" | 28 source="both" |
20 level="fatal" | 29 level="fatal" |
192 <param name="rdata_out" value="false"/> | 201 <param name="rdata_out" value="false"/> |
193 </section> | 202 </section> |
194 <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/> | 203 <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/> |
195 <output name="wallenius_tab"> | 204 <output name="wallenius_tab"> |
196 <assert_contents> | 205 <assert_contents> |
197 <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="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> |
198 <has_text_matching expression="GO:0000278.*0.01" /> | 207 <has_text_matching expression="GO:0000278.*0.01" /> |
199 </assert_contents> | 208 </assert_contents> |
200 </output> | 209 </output> |
201 </test> | 210 </test> |
202 <!-- Ensure getting GO categories works & also DE genes for GO terms--> | 211 <!-- Ensure getting GO categories works & also DE genes for GO terms--> |
224 <param name="cat_genes" value="true"/> | 233 <param name="cat_genes" value="true"/> |
225 <param name="rdata_out" value="false"/> | 234 <param name="rdata_out" value="false"/> |
226 </section> | 235 </section> |
227 <output name="wallenius_tab"> | 236 <output name="wallenius_tab"> |
228 <assert_contents> | 237 <assert_contents> |
229 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> | 238 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> |
230 <has_text_matching expression="GO:0005576.*9.0" /> | 239 <has_text_matching expression="GO:0005576.*0.9" /> |
231 </assert_contents> | 240 </assert_contents> |
232 </output> | 241 </output> |
233 <output name="cat_genes_tab"> | 242 <output name="cat_genes_tab"> |
234 <assert_contents> | 243 <assert_contents> |
235 <has_text_matching expression="Categories.*DEgenes" /> | 244 <has_text_matching expression="category.*de_genes" /> |
236 <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" /> | 245 <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" /> |
237 </assert_contents> | 246 </assert_contents> |
238 </output> | 247 </output> |
239 </test> | 248 </test> |
240 <!-- Ensure getting GO categories for another genome (zebrafish) works --> | 249 <!-- Ensure getting GO categories for another genome (zebrafish) works --> |
262 <param name="cat_genes" value="false"/> | 271 <param name="cat_genes" value="false"/> |
263 <param name="rdata_out" value="false"/> | 272 <param name="rdata_out" value="false"/> |
264 </section> | 273 </section> |
265 <output name="wallenius_tab"> | 274 <output name="wallenius_tab"> |
266 <assert_contents> | 275 <assert_contents> |
267 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> | 276 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> |
268 <has_text_matching expression="GO:0016569.*0.8" /> | 277 <has_text_matching expression="GO:0016569.*0.90" /> |
269 </assert_contents> | 278 </assert_contents> |
270 </output> | 279 </output> |
271 </test> | 280 </test> |
272 <!-- Ensure length bias plot works --> | 281 <!-- Ensure length bias plot works --> |
273 <test expect_num_outputs="2"> | 282 <test expect_num_outputs="2"> |
436 This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced. | 445 This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced. |
437 | 446 |
438 Example: | 447 Example: |
439 | 448 |
440 =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== | 449 =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== |
441 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p.adjust.over_rep* *p.adjust.under_rep* | 450 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p_adjust_over_rep* *p_adjust_under_rep* |
442 ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- -------------------- | 451 ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- -------------------- |
443 GO\:0005576 0.000054 0.999975 56 142 extracellular region CC 0.394825 1 | 452 GO\:0005576 0.000054 0.999975 56 142 extracellular region CC 0.394825 1 |
444 GO\:0005840 0.000143 0.999988 9 12 ribosome CC 0.394825 1 | 453 GO\:0005840 0.000143 0.999988 9 12 ribosome CC 0.394825 1 |
445 GO\:0044763 0.000252 0.999858 148 473 single-organism cellular process BP 0.394825 1 | 454 GO\:0044763 0.000252 0.999858 148 473 single-organism cellular process BP 0.394825 1 |
446 GO\:0044699 0.000279 0.999844 158 513 single-organism process BP 0.394825 1 | 455 GO\:0044699 0.000279 0.999844 158 513 single-organism process BP 0.394825 1 |