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comparison egsea.xml @ 2:ba2111ae6eb4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
author iuc
date Mon, 28 Jan 2019 18:39:06 -0500
parents 73281fbdf6c1
children 31ea4992b948
comparison
equal deleted inserted replaced
1:73281fbdf6c1 2:ba2111ae6eb4
1 <tool id="egsea" name="EGSEA" version="1.6.0.1"> 1 <tool id="egsea" name="EGSEA" version="1.8.0">
2 <description> easy and efficient ensemble gene set testing</description> 2 <description> easy and efficient ensemble gene set testing</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.0">bioconductor-egsea</requirement> 4 <requirement type="package" version="1.8.0">bioconductor-egsea</requirement>
5 <requirement type="package" version="1.4.4">r-optparse</requirement> 5 <requirement type="package" version="1.6.0">r-optparse</requirement>
6 <requirement type="package" version="0.2.15">r-rjson</requirement> 6 <requirement type="package" version="0.2.20">r-rjson</requirement>
7 <!--statmod is required for fry--> 7 <!--statmod is required for fry-->
8 <requirement type="package" version="1.4.30">r-statmod</requirement> 8 <requirement type="package" version="1.4.30">r-statmod</requirement>
9 </requirements> 9 </requirements>
10 <version_command><![CDATA[ 10 <version_command><![CDATA[
11 echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 11 echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
262 </data> 262 </data>
263 </outputs> 263 </outputs>
264 264
265 <tests> 265 <tests>
266 <!-- Ensure report is output --> 266 <!-- Ensure report is output -->
267 <test expect_num_outputs="1"> 267 <test expect_num_outputs="2">
268 <param name="non_commercial_use" value="True"/> 268 <param name="non_commercial_use" value="True"/>
269 <param name="format" value="matrix" /> 269 <param name="format" value="matrix" />
270 <param name="counts" value="il13.counts"/> 270 <param name="counts" value="il13.counts"/>
271 <param name="genes" value="il13.genes"/> 271 <param name="genes" value="il13.genes"/>
272 <repeat name="rep_factor"> 272 <repeat name="rep_factor">
275 </repeat> 275 </repeat>
276 <repeat name="rep_contrast"> 276 <repeat name="rep_contrast">
277 <param name="contrast" value="IL13Ant-IL13"/> 277 <param name="contrast" value="IL13Ant-IL13"/>
278 </repeat> 278 </repeat>
279 <output_collection name="outTables" count="1"> 279 <output_collection name="outTables" count="1">
280 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13.txt"/> 280 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
281 <assert_contents>
282 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
283 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
284 </assert_contents>
285 </element>
281 </output_collection> 286 </output_collection>
282 <output name="outReport"> 287 <output name="outReport">
283 <assert_contents> 288 <assert_contents>
284 <has_text text="Gene Set Testing Report"/> 289 <has_text text="Gene Set Testing Report"/>
285 </assert_contents> 290 </assert_contents>
286 </output> 291 </output>
287 </test> 292 </test>
288 <!-- Ensure factors file input works and Rscript is output--> 293 <!-- Ensure factors file input works and Rscript is output-->
294 <test expect_num_outputs="3">
295 <param name="non_commercial_use" value="True"/>
296 <param name="format" value="matrix"/>
297 <param name="counts" value="il13.counts"/>
298 <param name="genes" value="il13.genes"/>
299 <param name="ffile" value="yes"/>
300 <param name="finfo" value="il13.group"/>
301 <repeat name="rep_contrast">
302 <param name="contrast" value="IL13Ant-IL13" />
303 </repeat>
304 <param name="rscriptOpt" value="True"/>
305 <output name="outReport">
306 <assert_contents>
307 <has_text text="Gene Set Testing Report"/>
308 </assert_contents>
309 </output>
310 <output_collection name="outTables" count="1">
311 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
312 <assert_contents>
313 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
314 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
315 </assert_contents>
316 </element>
317 </output_collection>
318 <output name="outRscript">
319 <assert_contents>
320 <has_text_matching expression="save.image" />
321 </assert_contents>
322 </output>
323 </test>
324 <!-- Ensure two contrasts works -->
289 <test expect_num_outputs="2"> 325 <test expect_num_outputs="2">
290 <param name="non_commercial_use" value="True"/> 326 <param name="non_commercial_use" value="True"/>
291 <param name="format" value="matrix"/> 327 <param name="format" value="matrix"/>
292 <param name="counts" value="il13.counts"/> 328 <param name="counts" value="il13.counts"/>
293 <param name="genes" value="il13.genes"/> 329 <param name="genes" value="il13.genes"/>
294 <param name="ffile" value="yes"/> 330 <param name="ffile" value="yes"/>
295 <param name="finfo" value="il13.group"/> 331 <param name="finfo" value="il13.group"/>
296 <repeat name="rep_contrast"> 332 <repeat name="rep_contrast">
297 <param name="contrast" value="IL13Ant-IL13" />
298 </repeat>
299 <param name="rscriptOpt" value="True"/>
300 <output name="outReport">
301 <assert_contents>
302 <has_text text="Gene Set Testing Report"/>
303 </assert_contents>
304 </output>
305 <output_collection name="outTables" count="1">
306 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13.txt"/>
307 </output_collection>
308 <output name="outRscript" value="out_rscript.txt"/>
309 </test>
310 <!-- Ensure two contrasts works -->
311 <test expect_num_outputs="1">
312 <param name="non_commercial_use" value="True"/>
313 <param name="format" value="matrix"/>
314 <param name="counts" value="il13.counts"/>
315 <param name="genes" value="il13.genes"/>
316 <param name="ffile" value="yes"/>
317 <param name="finfo" value="il13.group"/>
318 <repeat name="rep_contrast">
319 <param name="contrast" value="IL13Ant-IL13"/> 333 <param name="contrast" value="IL13Ant-IL13"/>
320 </repeat> 334 </repeat>
321 <repeat name="rep_contrast"> 335 <repeat name="rep_contrast">
322 <param name="contrast" value="IL13-IL13Ant"/> 336 <param name="contrast" value="IL13-IL13Ant"/>
323 </repeat> 337 </repeat>
324 <output_collection name="outTables" count="3"> 338 <output_collection name="outTables" count="3">
325 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13.txt"/> 339 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
326 <element name="ranked-h-gene-sets-IL13-IL13Ant" ftype="tabular" file="ranked-h-gene-sets-IL13-IL13Ant.txt"/> 340 <assert_contents>
327 <element name="ranked-h-gene-sets-IL13-IL13Ant" ftype="tabular" file="ranked-h-gene-sets-compare.txt"/> 341 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
342 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
343 </assert_contents>
344 </element>
345 <element name="ranked-h-gene-sets-IL13-IL13Ant" ftype="tabular">
346 <assert_contents>
347 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
348 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
349 </assert_contents>
350 </element>
328 </output_collection> 351 </output_collection>
329 </test> 352 </test>
330 <!-- Ensure two factors works --> 353 <!-- Ensure two factors works -->
331 <test expect_num_outputs="1"> 354 <test expect_num_outputs="2">
332 <param name="non_commercial_use" value="True"/> 355 <param name="non_commercial_use" value="True"/>
333 <param name="format" value="matrix"/> 356 <param name="format" value="matrix"/>
334 <param name="counts" value="il13.counts"/> 357 <param name="counts" value="il13.counts"/>
335 <param name="genes" value="il13.genes"/> 358 <param name="genes" value="il13.genes"/>
336 <param name="ffile" value="yes"/> 359 <param name="ffile" value="yes"/>
337 <param name="finfo" value="il13.group_batch"/> 360 <param name="finfo" value="il13.group_batch"/>
338 <repeat name="rep_contrast"> 361 <repeat name="rep_contrast">
339 <param name="contrast" value="IL13Ant-IL13"/> 362 <param name="contrast" value="IL13Ant-IL13"/>
340 </repeat> 363 </repeat>
341 <output_collection name="outTables" count="1"> 364 <output_collection name="outTables" count="1">
342 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/> 365 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
366 <assert_contents>
367 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
368 <has_text_matching expression="1.*M5928.*HALLMARK_MYC_TARGETS_V2.*53/58.*6.7" />
369 </assert_contents>
370 </element>
343 </output_collection> 371 </output_collection>
344 </test> 372 </test>
345 <!-- Ensure all gene set methods work --> 373 <!-- Ensure all gene set methods work -->
346 <test expect_num_outputs="1"> 374 <test expect_num_outputs="2">
347 <param name="non_commercial_use" value="True"/> 375 <param name="non_commercial_use" value="True"/>
348 <param name="format" value="matrix"/> 376 <param name="format" value="matrix"/>
349 <param name="counts" value="il13.counts"/> 377 <param name="counts" value="il13.counts"/>
350 <param name="genes" value="il13.genes"/> 378 <param name="genes" value="il13.genes"/>
351 <param name="ffile" value="yes"/> 379 <param name="ffile" value="yes"/>
353 <repeat name="rep_contrast"> 381 <repeat name="rep_contrast">
354 <param name="contrast" value="IL13Ant-IL13"/> 382 <param name="contrast" value="IL13Ant-IL13"/>
355 </repeat> 383 </repeat>
356 <param name="base_methods" value="camera,safe,gage,zscore,gsva,globaltest,ora,ssgsea,padog,plage,fry,roast"/> 384 <param name="base_methods" value="camera,safe,gage,zscore,gsva,globaltest,ora,ssgsea,padog,plage,fry,roast"/>
357 <output_collection name="outTables" count="1"> 385 <output_collection name="outTables" count="1">
358 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch_all.txt"/> 386 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
387 <assert_contents>
388 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
389 <has_text_matching expression="1.*M5928.*HALLMARK_MYC_TARGETS_V2.*53/58.*2.6" />
390 </assert_contents>
391 </element>
359 </output_collection> 392 </output_collection>
360 </test> 393 </test>
361 <!-- Ensure KEGG updated works --> 394 <!-- Ensure KEGG updated works -->
362 <test expect_num_outputs="1"> 395 <test expect_num_outputs="2">
363 <param name="non_commercial_use" value="True"/> 396 <param name="non_commercial_use" value="True"/>
364 <param name="format" value="matrix"/> 397 <param name="format" value="matrix"/>
365 <param name="counts" value="il13.counts"/> 398 <param name="counts" value="il13.counts"/>
366 <param name="genes" value="il13.genes"/> 399 <param name="genes" value="il13.genes"/>
367 <param name="ffile" value="yes"/> 400 <param name="ffile" value="yes"/>
370 <param name="contrast" value="IL13Ant-IL13"/> 403 <param name="contrast" value="IL13Ant-IL13"/>
371 </repeat> 404 </repeat>
372 <param name="keggdb_gsets" value="keggmet"/> 405 <param name="keggdb_gsets" value="keggmet"/>
373 <param name="kegg_updated" value="True"/> 406 <param name="kegg_updated" value="True"/>
374 <output_collection name="outTables" count="2"> 407 <output_collection name="outTables" count="2">
375 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/> 408 <element name="ranked-kegg-gene-sets-IL13Ant-IL13" ftype="tabular">
376 <element name="ranked-kegg-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-kegg-gene-sets-IL13Ant-IL13.txt"/> 409 <assert_contents>
410 <has_text_matching expression="Rank.*ID.*GeneSet.*NumGenes.*Type.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
411 <has_text_matching expression="1.*hsa00290.*Valine, leucine and isoleucine biosynthesis.*4/4.*Metabolism.*5.1" />
412 </assert_contents>
413 </element>
414 </output_collection>
415 </test>
416 <!-- Ensure individual counts files works -->
417 <test expect_num_outputs="2">
418 <param name="non_commercial_use" value="True"/>
419 <param name="format" value="files" />
420 <repeat name="rep_factor">
421 <param name="factorName" value="Treatment"/>
422 <repeat name="rep_group">
423 <param name="groupName" value="IL13"/>
424 <param name="countsFile" value="IL13-1.counts,IL13-2.counts,IL13-3.counts"/>
425 </repeat>
426 <repeat name="rep_group">
427 <param name="groupName" value="IL13Ant"/>
428 <param name="countsFile" value="IL13Ant-1.counts,IL13Ant-2.counts"/>
429 </repeat>
430 </repeat>
431 <repeat name="rep_factor">
432 <param name="factorName" value="Batch"/>
433 <repeat name="rep_group">
434 <param name="groupName" value="b1"/>
435 <param name="countsFile" value="IL13-1.counts,IL13Ant-1.counts"/>
436 </repeat>
437 <repeat name="rep_group">
438 <param name="groupName" value="b2"/>
439 <param name="countsFile" value="IL13-2.counts,IL13-3.counts,IL13Ant-2.counts"/>
440 </repeat>
441 </repeat>
442 <param name="genes" value="il13.genes"/>
443 <repeat name="rep_contrast">
444 <param name="contrast" value="IL13Ant-IL13"/>
445 </repeat>
446 <output_collection name="outTables" count="1">
447 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
448 <assert_contents>
449 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
450 <has_text_matching expression="1.*M5928.*HALLMARK_MYC_TARGETS_V2.*53/58.*6.7" />
451 </assert_contents>
452 </element>
377 </output_collection> 453 </output_collection>
378 </test> 454 </test>
379 </tests> 455 </tests>
380 456
381 <help><![CDATA[ 457 <help><![CDATA[
407 483
408 ----- 484 -----
409 485
410 **Inputs** 486 **Inputs**
411 487
412 **Counts Matrix** 488 **Counts Data**
413 489
414 This tool requires a counts matrix (counts table) containing the raw RNA-seq read counts. The first column must contain Entrez Gene IDs that are unique (not repeated) within the counts file. Entrez IDs can be obtained from the **annotateMyIDs** Galaxy tool. 490 This tool requires a counts matrix (counts table) containing the raw RNA-seq read counts. The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels. The first column must contain Entrez Gene IDs that are unique (not repeated) within the counts file. Entrez IDs can be obtained from the **annotateMyIDs** Galaxy tool. Genes with low counts should be removed, such as in the filtered counts matrix that can be output from the **limma** tool.
415 491
416 Example: 492 Example - **Separate Count Files**:
493
494 =============== ==========
495 EntrezID **WT1**
496 =============== ==========
497 1 71
498 1000 3
499 10000 2310
500 100009605 3
501 100009613 9
502 =============== ==========
503
504 Example - **Single Count Matrix**:
417 505
418 =============== ========== ========== ========== ========= ========= ========= 506 =============== ========== ========== ========== ========= ========= =========
419 EntrezID **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3** 507 EntrezID **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
420 =============== ========== ========== ========== ========= ========= ========= 508 =============== ========== ========== ========== ========= ========= =========
421 1 71 73 69 36 22 28 509 1 71 73 69 36 22 28
425 100009613 9 11 4 13 6 10 513 100009613 9 11 4 13 6 10
426 =============== ========== ========== ========== ========= ========= ========= 514 =============== ========== ========== ========== ========= ========= =========
427 515
428 **Factor Information** 516 **Factor Information**
429 517
430 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors e.g Batch. 518 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors e.g Batch.
431 519
432 Example: 520 Example:
433 521
434 ========== ============ ========= 522 ========== ============ =========
435 **Sample** **Genotype** **Batch** 523 **Sample** **Genotype** **Batch**
442 Mut3 Mut b3 530 Mut3 Mut b3
443 ========== ============ ========= 531 ========== ============ =========
444 532
445 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model. 533 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
446 534
447 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas. 535 *Groups:* The names of the groups for the factor. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
448 536
449 **Symbols Mapping file** 537 **Symbols Mapping file**
450 538
451 A file containing the Gene Symbol for each Entrez Gene ID. The first column must be the Entrez Gene IDs and the second column must be the Gene Symbols. It is used for the heatmap visualization. The number of rows should match that of the Counts Matrix. 539 A file containing the Gene Symbol for each Entrez Gene ID. The first column must be the Entrez Gene IDs and the second column must be the Gene Symbols. It is used for the heatmap visualization. The number of rows should match that of the Counts Matrix.
452 540