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comparison edger.xml @ 2:3de72f1f78aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
author iuc
date Thu, 19 Apr 2018 17:26:20 -0400
parents c469357cf454
children 2aa9dd87aad3
comparison
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1:c469357cf454 2:3de72f1f78aa
1 <tool id="edger" name="edgeR" version="3.20.7.0"> 1 <tool id="edger" name="edgeR" version="3.20.7.1">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement> 7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
8 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
8 <requirement type="package" version="0.2.15">r-rjson</requirement> 9 <requirement type="package" version="0.2.15">r-rjson</requirement>
9 <requirement type="package" version="1.20.0">r-getopt</requirement> 10 <requirement type="package" version="1.20.0">r-getopt</requirement>
10 <requirement type="package" version="1.4.30">r-statmod</requirement> 11 <requirement type="package" version="1.4.30">r-statmod</requirement>
11 <!-- required for alpha function used with plotMD --> 12 <!-- required for alpha function used with plotMD -->
12 <requirement type="package" version="0.5.0">r-scales</requirement> 13 <requirement type="package" version="0.5.0">r-scales</requirement>
13 </requirements> 14 </requirements>
14 15
15 <version_command><![CDATA[ 16 <version_command><![CDATA[
16 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$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: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 17 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$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: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
17 ]]></version_command> 18 ]]></version_command>
18 19
19 <command detect_errors="exit_code"><![CDATA[ 20 <command detect_errors="exit_code"><![CDATA[
20 #import json 21 #import json
21 Rscript '$__tool_directory__/edger.R' 22 Rscript '$__tool_directory__/edger.R'
92 && 93 &&
93 mkdir ./output_dir 94 mkdir ./output_dir
94 95
95 && 96 &&
96 cp '$outReport.files_path'/*.tsv output_dir/ 97 cp '$outReport.files_path'/*.tsv output_dir/
98
99 #if $out.rscript:
100 && cp '$__tool_directory__/edger.R' '$rscript'
101 #end if
97 ]]></command> 102 ]]></command>
98 103
99 <inputs> 104 <inputs>
100 105
101 <!-- Counts and Factors --> 106 <!-- Counts and Factors -->
220 <section name="out" expanded="false" title="Output Options"> 225 <section name="out" expanded="false" title="Output Options">
221 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 226 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
222 label="Output Normalised Counts Table?" 227 label="Output Normalised Counts Table?"
223 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> 228 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
224 </param> 229 </param>
230 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
225 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" 231 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
226 label="Output RData file?" 232 label="Output RData file?"
227 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No"> 233 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No">
228 </param> 234 </param>
229 </section> 235 </section>
257 <outputs> 263 <outputs>
258 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" /> 264 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
259 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> 265 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
260 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> 266 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
261 </collection> 267 </collection>
268 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
269 <filter>out['rscript']</filter>
270 </data>
262 </outputs> 271 </outputs>
263 272
264 <tests> 273 <tests>
265 <!-- Ensure report is output --> 274 <!-- Ensure report is output -->
266 <test> 275 <test>
276 <repeat name="rep_contrast"> 285 <repeat name="rep_contrast">
277 <param name="contrast" value="WT-Mut" /> 286 <param name="contrast" value="WT-Mut" />
278 </repeat> 287 </repeat>
279 <param name="normalisationOption" value="TMM" /> 288 <param name="normalisationOption" value="TMM" />
280 <output_collection name="outTables" count="2"> 289 <output_collection name="outTables" count="2">
281 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT.tsv" /> 290 <element name="edgeR_Mut-WT" ftype="tabular" >
282 <element name="edgeR_WT-Mut" ftype="tabular" file="edgeR_WT-Mut.tsv" /> 291 <assert_contents>
292 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
293 <has_text_matching expression="11304.*0.4582" />
294 </assert_contents>
295 </element>
296 <element name="edgeR_WT-Mut" ftype="tabular" >
297 <assert_contents>
298 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
299 <has_text_matching expression="11304.*-0.4582" />
300 </assert_contents>
301 </element>
283 </output_collection> 302 </output_collection>
284 <output name="outReport" > 303 <output name="outReport" >
285 <assert_contents> 304 <assert_contents>
286 <has_text text="edgeR Analysis Output" /> 305 <has_text text="edgeR Analysis Output" />
287 <has_text text="quasi-likelihood" /> 306 <has_text text="quasi-likelihood" />
303 <repeat name="rep_contrast"> 322 <repeat name="rep_contrast">
304 <param name="contrast" value="Mut-WT" /> 323 <param name="contrast" value="Mut-WT" />
305 </repeat> 324 </repeat>
306 <param name="normalisationOption" value="TMM" /> 325 <param name="normalisationOption" value="TMM" />
307 <output_collection name="outTables" count="1"> 326 <output_collection name="outTables" count="1">
308 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_anno.tsv" /> 327 <element name="edgeR_Mut-WT" ftype="tabular" >
328 <assert_contents>
329 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" />
330 <has_text_matching expression="11304.*Abca4.*0.4582" />
331 </assert_contents>
332 </element>
309 </output_collection> 333 </output_collection>
310 </test> 334 </test>
311 <!-- Ensure RData file can be output --> 335 <!-- Ensure RScript and RData file can be output -->
312 <test> 336 <test>
313 <param name="format" value="matrix" /> 337 <param name="format" value="matrix" />
338 <param name="rscript" value="True"/>
314 <param name="rdaOption" value="true" /> 339 <param name="rdaOption" value="true" />
315 <param name="counts" value="matrix.txt" /> 340 <param name="counts" value="matrix.txt" />
316 <repeat name="rep_factor"> 341 <repeat name="rep_factor">
317 <param name="factorName" value="Genotype"/> 342 <param name="factorName" value="Genotype"/>
318 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 343 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
324 <output name="outReport" > 349 <output name="outReport" >
325 <assert_contents> 350 <assert_contents>
326 <has_text text="RData" /> 351 <has_text text="RData" />
327 </assert_contents> 352 </assert_contents>
328 </output> 353 </output>
354 <output name="rscript" value="out_rscript.txt"/>
329 </test> 355 </test>
330 <!-- Ensure secondary factors work --> 356 <!-- Ensure secondary factors work -->
331 <test> 357 <test>
332 <param name="format" value="matrix" /> 358 <param name="format" value="matrix" />
333 <param name="counts" value="matrix.txt" /> 359 <param name="counts" value="matrix.txt" />
342 <repeat name="rep_contrast"> 368 <repeat name="rep_contrast">
343 <param name="contrast" value="Mut-WT" /> 369 <param name="contrast" value="Mut-WT" />
344 </repeat> 370 </repeat>
345 <param name="normalisationOption" value="TMM" /> 371 <param name="normalisationOption" value="TMM" />
346 <output_collection name="outTables" count="1" > 372 <output_collection name="outTables" count="1" >
347 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact.tsv" /> 373 <element name="edgeR_Mut-WT" ftype="tabular" >
374 <assert_contents>
375 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
376 <has_text_matching expression="11304.*0.4584" />
377 </assert_contents>
378 </element>
348 </output_collection> 379 </output_collection>
349 </test> 380 </test>
350 <!-- Ensure factors file input works --> 381 <!-- Ensure factors file input works -->
351 <test> 382 <test>
352 <param name="format" value="matrix" /> 383 <param name="format" value="matrix" />
356 <repeat name="rep_contrast"> 387 <repeat name="rep_contrast">
357 <param name="contrast" value="Mut-WT" /> 388 <param name="contrast" value="Mut-WT" />
358 </repeat> 389 </repeat>
359 <param name="normalisationOption" value="TMM" /> 390 <param name="normalisationOption" value="TMM" />
360 <output_collection name="outTables" count="1"> 391 <output_collection name="outTables" count="1">
361 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact.tsv" /> 392 <element name="edgeR_Mut-WT" ftype="tabular" >
393 <assert_contents>
394 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
395 <has_text_matching expression="11304.*0.4584" />
396 </assert_contents>
397 </element>
362 </output_collection> 398 </output_collection>
363 </test> 399 </test>
364 <!-- Ensure normalised counts file output works--> 400 <!-- Ensure normalised counts file output works-->
365 <test> 401 <test>
366 <param name="format" value="matrix" /> 402 <param name="format" value="matrix" />
373 <repeat name="rep_contrast"> 409 <repeat name="rep_contrast">
374 <param name="contrast" value="Mut-WT" /> 410 <param name="contrast" value="Mut-WT" />
375 </repeat> 411 </repeat>
376 <param name="normalisationOption" value="TMM" /> 412 <param name="normalisationOption" value="TMM" />
377 <output_collection name="outTables" count="2"> 413 <output_collection name="outTables" count="2">
378 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT.tsv" /> 414 <element name="edgeR_Mut-WT" ftype="tabular" >
379 <element name="edgeR_normcounts" ftype="tabular" file="edgeR_normcounts.tsv" /> 415 <assert_contents>
416 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
417 <has_text_matching expression="11304.*0.4582" />
418 </assert_contents>
419 </element>
420 <element name="edgeR_normcounts" ftype="tabular" >
421 <assert_contents>
422 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
423 <has_text_matching expression="11304.*15.7535" />
424 </assert_contents>
425 </element>
380 </output_collection> 426 </output_collection>
381 </test> 427 </test>
382 <!-- Ensure likelihood ratio option works --> 428 <!-- Ensure likelihood ratio option works -->
383 <test> 429 <test>
384 <param name="format" value="matrix" /> 430 <param name="format" value="matrix" />
436 <repeat name="rep_contrast"> 482 <repeat name="rep_contrast">
437 <param name="contrast" value="WT-Mut" /> 483 <param name="contrast" value="WT-Mut" />
438 </repeat> 484 </repeat>
439 <param name="normCounts" value="true" /> 485 <param name="normCounts" value="true" />
440 <output_collection name="outTables" count="3"> 486 <output_collection name="outTables" count="3">
441 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact_anno.tsv" /> 487 <element name="edgeR_Mut-WT" ftype="tabular" >
442 <element name="edgeR_WT-Mut" ftype="tabular" file="edgeR_WT-Mut_2fact_anno.tsv" /> 488 <assert_contents>
443 <element name="edgeR_normcounts" ftype="tabular" file="edgeR_normcounts_anno.tsv" /> 489 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" />
490 <has_text_matching expression="11304.*Abca4.*0.4584" />
491 </assert_contents>
492 </element>
493 <element name="edgeR_WT-Mut" ftype="tabular" >
494 <assert_contents>
495 <has_text_matching expression="logFC.*logCPM.*F.*PValue.*FDR" />
496 <has_text_matching expression="11304.*Abca4.*-0.4584" />
497 </assert_contents>
498 </element>
499 <element name="edgeR_normcounts" ftype="tabular" >
500 <assert_contents>
501 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
502 <has_text_matching expression="11304.*Abca4.*15.7535" />
503 </assert_contents>
504 </element>
444 </output_collection> 505 </output_collection>
445 </test> 506 </test>
446 <!-- Ensure filtering on CPM in Mnimum Samples works --> 507 <!-- Ensure filtering on CPM in Mnimum Samples works -->
447 <test> 508 <test>
448 <param name="format" value="matrix" /> 509 <param name="format" value="matrix" />
467 <not_has_text text="after summing counts for all samples" /> 528 <not_has_text text="after summing counts for all samples" />
468 <not_has_text text="counts in at least" /> 529 <not_has_text text="counts in at least" />
469 </assert_contents> 530 </assert_contents>
470 </output> 531 </output>
471 <output_collection name="outTables" count="1" > 532 <output_collection name="outTables" count="1" >
472 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" /> 533 <element name="edgeR_Mut-WT" ftype="tabular" >
534 <assert_contents>
535 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
536 <has_text_matching expression="11304.*0.4568" />
537 <not_has_text text="-0.0682" />
538 </assert_contents>
539 </element>
473 </output_collection> 540 </output_collection>
474 </test> 541 </test>
475 <!-- Ensure filtering on Count in Minmum Samples works --> 542 <!-- Ensure filtering on Count in Minmum Samples works -->
476 <test> 543 <test>
477 <param name="format" value="matrix" /> 544 <param name="format" value="matrix" />
495 <not_has_text text="after summing counts for all samples" /> 562 <not_has_text text="after summing counts for all samples" />
496 <not_has_text text="CPM in at least" /> 563 <not_has_text text="CPM in at least" />
497 </assert_contents> 564 </assert_contents>
498 </output> 565 </output>
499 <output_collection name="outTables" count="1" > 566 <output_collection name="outTables" count="1" >
500 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" /> 567 <element name="edgeR_Mut-WT" ftype="tabular" >
568 <assert_contents>
569 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
570 <has_text_matching expression="11304.*0.4568" />
571 <not_has_text text="-0.0682" />
572 </assert_contents>
573 </element>
574
501 </output_collection> 575 </output_collection>
502 </test> 576 </test>
503 <!-- Ensure filtering on Total Count works --> 577 <!-- Ensure filtering on Total Count works -->
504 <test> 578 <test>
505 <param name="format" value="matrix" /> 579 <param name="format" value="matrix" />
525 <not_has_text text="counts in at least" /> 599 <not_has_text text="counts in at least" />
526 <not_has_text text="CPM in at least" /> 600 <not_has_text text="CPM in at least" />
527 </assert_contents> 601 </assert_contents>
528 </output> 602 </output>
529 <output_collection name="outTables" count="1" > 603 <output_collection name="outTables" count="1" >
530 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" /> 604 <element name="edgeR_Mut-WT" ftype="tabular" >
605 <assert_contents>
606 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
607 <has_text_matching expression="11304.*0.4568" />
608 <not_has_text text="-0.0682" />
609 </assert_contents>
610 </element>
531 </output_collection> 611 </output_collection>
532 </test> 612 </test>
533 </tests> 613 </tests>
534 614
535 <help><![CDATA[ 615 <help><![CDATA[
714 * a HTML report with plots and additional information 794 * a HTML report with plots and additional information
715 795
716 Optionally, under **Output Options** you can choose to output 796 Optionally, under **Output Options** you can choose to output
717 797
718 * a normalised counts table 798 * a normalised counts table
799 * the R script used by this tool
719 * an RData file 800 * an RData file
720 801
721 ----- 802 -----
722 803
723 **Citations** 804 **Citations**