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comparison limma_voom.xml @ 4:47cf8073da69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
author iuc
date Sun, 29 Apr 2018 17:36:26 -0400
parents 895d310ddb21
children ffa5acf8826c
comparison
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3:895d310ddb21 4:47cf8073da69
1 <tool id="limma_voom" name="limma" version="3.34.6.0"> 1 <tool id="limma_voom" name="limma" version="3.34.9.0">
2 <description> 2 <description>
3 Perform differential expression with limma-voom or limma-trend 3 Perform differential expression with limma-voom or limma-trend
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.34.6">bioconductor-limma</requirement> 7 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement> 8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
9 <requirement type="package" version="1.4.30">r-statmod</requirement> 9 <requirement type="package" version="1.4.30">r-statmod</requirement>
10 <requirement type="package" version="0.5.0">r-scales</requirement> 10 <requirement type="package" version="0.5.0">r-scales</requirement>
11 <requirement type="package" version="0.2.15">r-rjson</requirement> 11 <requirement type="package" version="0.2.15">r-rjson</requirement>
12 <requirement type="package" version="1.20.0">r-getopt</requirement> 12 <requirement type="package" version="1.20.0">r-getopt</requirement>
100 && 100 &&
101 mkdir ./output_dir 101 mkdir ./output_dir
102 102
103 && 103 &&
104 cp '$outReport.files_path'/*.tsv output_dir/ 104 cp '$outReport.files_path'/*.tsv output_dir/
105
106 #if $out.rscript:
107 && cp '$__tool_directory__/limma_voom.R' '$rscript'
108 #end if
105 ]]></command> 109 ]]></command>
106 110
107 <inputs> 111 <inputs>
108 112
109 <!-- DE Method Option --> 113 <!-- DE Method Option -->
136 <valid initial="string.letters,string.digits"><add value="_" /></valid> 140 <valid initial="string.letters,string.digits"><add value="_" /></valid>
137 </sanitizer> 141 </sanitizer>
138 </param> 142 </param>
139 <repeat name="rep_group" title="Group" min="2" default="2"> 143 <repeat name="rep_group" title="Group" min="2" default="2">
140 <param name="groupName" type="text" label="Name" 144 <param name="groupName" type="text" label="Name"
141 help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive)."> 145 help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
142 <sanitizer> 146 <sanitizer>
143 <valid initial="string.letters,string.digits"><add value="_" /></valid> 147 <valid initial="string.letters,string.digits"><add value="_" /></valid>
144 </sanitizer> 148 </sanitizer>
145 </param> 149 </param>
146 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 150 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
147 </repeat> 151 </repeat>
148 </repeat> 152 </repeat>
149 </when> 153 </when>
150 154
151 <when value="matrix"> 155 <when value="matrix">
243 <section name="out" expanded="false" title="Output Options"> 247 <section name="out" expanded="false" title="Output Options">
244 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 248 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
245 label="Output Normalised Counts Table?" 249 label="Output Normalised Counts Table?"
246 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> 250 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
247 </param> 251 </param>
252 <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"/>
248 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" 253 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
249 label="Output RData file?" 254 label="Output RData file?"
250 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"> 255 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">
251 </param> 256 </param>
252 </section> 257 </section>
279 <outputs> 284 <outputs>
280 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" /> 285 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
281 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> 286 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
282 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> 287 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
283 </collection> 288 </collection>
289 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
290 <filter>out['rscript']</filter>
291 </data>
284 </outputs> 292 </outputs>
285 293
286 <tests> 294 <tests>
287 <!-- Ensure report is output --> 295 <!-- Ensure report is output -->
288 <test> 296 <test>
298 <repeat name="rep_contrast"> 306 <repeat name="rep_contrast">
299 <param name="contrast" value="WT-Mut" /> 307 <param name="contrast" value="WT-Mut" />
300 </repeat> 308 </repeat>
301 <param name="normalisationOption" value="TMM" /> 309 <param name="normalisationOption" value="TMM" />
302 <output_collection name="outTables" count="2"> 310 <output_collection name="outTables" count="2">
303 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" /> 311 <element name="limma-voom_Mut-WT" ftype="tabular" >
304 <element name="limma-voom_WT-Mut" ftype="tabular" file="limma-voom_WT-Mut.tsv" /> 312 <assert_contents>
313 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
314 <has_text_matching expression="11304.*0.4573" />
315 </assert_contents>
316 </element>
317 <element name="limma-voom_WT-Mut" ftype="tabular" >
318 <assert_contents>
319 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
320 <has_text_matching expression="11304.*-0.4573" />
321 </assert_contents>
322 </element>
305 </output_collection> 323 </output_collection>
306 <output name="outReport" > 324 <output name="outReport" >
307 <assert_contents> 325 <assert_contents>
308 <has_text text="Limma Analysis Output" /> 326 <has_text text="Limma Analysis Output" />
309 <not_has_text text="RData" /> 327 <not_has_text text="RData" />
310 </assert_contents> 328 </assert_contents>
311 </output> 329 </output>
312 </test> 330 </test>
313 <!-- Ensure annotation file input works --> 331 <!-- Ensure annotation file input works -->
314 <test> 332 <test>
315 <param name="format" value="matrix" /> 333 <param name="format" value="matrix" />
316 <param name="annoOpt" value="yes" /> 334 <param name="annoOpt" value="yes" />
317 <param name="geneanno" value="anno.txt" /> 335 <param name="geneanno" value="anno.txt" />
323 <repeat name="rep_contrast"> 341 <repeat name="rep_contrast">
324 <param name="contrast" value="Mut-WT" /> 342 <param name="contrast" value="Mut-WT" />
325 </repeat> 343 </repeat>
326 <param name="normalisationOption" value="TMM" /> 344 <param name="normalisationOption" value="TMM" />
327 <output_collection name="outTables" count="1"> 345 <output_collection name="outTables" count="1">
328 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_anno.tsv" /> 346 <element name="limma-voom_Mut-WT" ftype="tabular" >
347 <assert_contents>
348 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
349 <has_text_matching expression="11304.*Abca4.*0.4573" />
350 </assert_contents>
351 </element>
329 </output_collection> 352 </output_collection>
330 </test> 353 </test>
331 <!-- Ensure RData file can be output --> 354 <!-- Ensure Rscript and RData file can be output -->
332 <test> 355 <test>
333 <param name="format" value="matrix" /> 356 <param name="format" value="matrix" />
357 <param name="rscript" value="True"/>
334 <param name="rdaOption" value="true" /> 358 <param name="rdaOption" value="true" />
335 <param name="counts" value="matrix.txt" /> 359 <param name="counts" value="matrix.txt" />
336 <repeat name="rep_factor"> 360 <repeat name="rep_factor">
337 <param name="factorName" value="Genotype"/> 361 <param name="factorName" value="Genotype"/>
338 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 362 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
344 <output name="outReport" > 368 <output name="outReport" >
345 <assert_contents> 369 <assert_contents>
346 <has_text text="RData" /> 370 <has_text text="RData" />
347 </assert_contents> 371 </assert_contents>
348 </output> 372 </output>
373 <output name="rscript" value="out_rscript.txt"/>
349 </test> 374 </test>
350 <!-- Ensure secondary factors work --> 375 <!-- Ensure secondary factors work -->
351 <test> 376 <test>
352 <param name="format" value="matrix" /> 377 <param name="format" value="matrix" />
353 <param name="counts" value="matrix.txt" /> 378 <param name="counts" value="matrix.txt" />
362 <repeat name="rep_contrast"> 387 <repeat name="rep_contrast">
363 <param name="contrast" value="Mut-WT" /> 388 <param name="contrast" value="Mut-WT" />
364 </repeat> 389 </repeat>
365 <param name="normalisationOption" value="TMM" /> 390 <param name="normalisationOption" value="TMM" />
366 <output_collection name="outTables" count="1" > 391 <output_collection name="outTables" count="1" >
367 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_2fact.tsv" /> 392 <element name="limma-voom_Mut-WT" ftype="tabular" >
393 <assert_contents>
394 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
395 <has_text_matching expression="11304.*0.4590" />
396 </assert_contents>
397 </element>
368 </output_collection> 398 </output_collection>
369 </test> 399 </test>
370 <!-- Ensure factors file input works --> 400 <!-- Ensure factors file input works -->
371 <test> 401 <test>
372 <param name="format" value="matrix" /> 402 <param name="format" value="matrix" />
376 <repeat name="rep_contrast"> 406 <repeat name="rep_contrast">
377 <param name="contrast" value="Mut-WT" /> 407 <param name="contrast" value="Mut-WT" />
378 </repeat> 408 </repeat>
379 <param name="normalisationOption" value="TMM" /> 409 <param name="normalisationOption" value="TMM" />
380 <output_collection name="outTables" count="1"> 410 <output_collection name="outTables" count="1">
381 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_2fact.tsv" /> 411 <element name="limma-voom_Mut-WT" ftype="tabular" >
412 <assert_contents>
413 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
414 <has_text_matching expression="11304.*0.4590" />
415 </assert_contents>
416 </element>
382 </output_collection> 417 </output_collection>
383 </test> 418 </test>
384 <!-- Ensure normalised counts file output works--> 419 <!-- Ensure normalised counts file output works-->
385 <test> 420 <test>
386 <param name="format" value="matrix" /> 421 <param name="format" value="matrix" />
393 <repeat name="rep_contrast"> 428 <repeat name="rep_contrast">
394 <param name="contrast" value="Mut-WT" /> 429 <param name="contrast" value="Mut-WT" />
395 </repeat> 430 </repeat>
396 <param name="normalisationOption" value="TMM" /> 431 <param name="normalisationOption" value="TMM" />
397 <output_collection name="outTables" count="2"> 432 <output_collection name="outTables" count="2">
398 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" /> 433 <element name="limma-voom_Mut-WT" ftype="tabular" >
399 <element name="limma-voom_normcounts" ftype="tabular" file="limma-voom_normcounts.tsv" /> 434 <assert_contents>
435 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
436 <has_text_matching expression="11304.*0.4573" />
437 </assert_contents>
438 </element>
439 <element name="limma-voom_normcounts" ftype="tabular" >
440 <assert_contents>
441 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
442 <has_text_matching expression="11304.*15.7545" />
443 </assert_contents>
444 </element>
400 </output_collection> 445 </output_collection>
401 </test> 446 </test>
402 <!-- Ensure multiple counts files input works --> 447 <!-- Ensure multiple counts files input works -->
403 <test> 448 <test>
404 <param name="format" value="files" /> 449 <param name="format" value="files" />
436 <repeat name="rep_contrast"> 481 <repeat name="rep_contrast">
437 <param name="contrast" value="WT-Mut" /> 482 <param name="contrast" value="WT-Mut" />
438 </repeat> 483 </repeat>
439 <param name="normCounts" value="true" /> 484 <param name="normCounts" value="true" />
440 <output_collection name="outTables" count="3"> 485 <output_collection name="outTables" count="3">
441 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_2fact_anno.tsv" /> 486 <element name="limma-voom_Mut-WT" ftype="tabular" >
442 <element name="limma-voom_WT-Mut" ftype="tabular" file="limma-voom_WT-Mut_2fact_anno.tsv" /> 487 <assert_contents>
443 <element name="limma-voom_normcounts" ftype="tabular" file="limma-voom_normcounts_anno.tsv" /> 488 <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
489 <has_text_matching expression="11304.*Abca4.*0.4590" />
490 </assert_contents>
491 </element>
492 <element name="limma-voom_WT-Mut" ftype="tabular" >
493 <assert_contents>
494 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
495 <has_text_matching expression="11304.*Abca4.*-0.4590" />
496 </assert_contents>
497 </element>
498 <element name="limma-voom_normcounts" ftype="tabular" >
499 <assert_contents>
500 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
501 <has_text_matching expression="11304.*Abca4.*15.7545" />
502 </assert_contents>
503 </element>
444 </output_collection> 504 </output_collection>
445 </test> 505 </test>
446 <!-- Ensure limma-trend option works --> 506 <!-- Ensure limma-trend option works -->
447 <test> 507 <test>
448 <param name="format" value="matrix" /> 508 <param name="format" value="matrix" />
461 <assert_contents> 521 <assert_contents>
462 <has_text text="The limma-trend method was used" /> 522 <has_text text="The limma-trend method was used" />
463 </assert_contents> 523 </assert_contents>
464 </output> 524 </output>
465 <output_collection name="outTables" count="1"> 525 <output_collection name="outTables" count="1">
466 <element name="limma-trend_Mut-WT" ftype="tabular" file="limma-trend_Mut-WT.tsv" /> 526 <element name="limma-trend_Mut-WT" ftype="tabular" >
527 <assert_contents>
528 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
529 <has_text_matching expression="11304.*0.4540" />
530 </assert_contents>
531 </element>
532 </output_collection>
533 </test>
534 <!-- Ensure limma-trend option with annotation works -->
535 <test>
536 <param name="format" value="matrix" />
537 <param name="counts" value="matrix.txt" />
538 <param name="annoOpt" value="yes" />
539 <param name="geneanno" value="anno.txt" />
540 <repeat name="rep_factor">
541 <param name="factorName" value="Genotype"/>
542 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
543 </repeat>
544 <repeat name="rep_contrast">
545 <param name="contrast" value="Mut-WT" />
546 </repeat>
547 <param name="normalisationOption" value="TMM" />
548 <param name="de_select" value="trend" />
549 <param name="rdaOption" value="true" />
550 <output name="outReport" >
551 <assert_contents>
552 <has_text text="The limma-trend method was used" />
553 </assert_contents>
554 </output>
555 <output_collection name="outTables" count="1">
556 <element name="limma-trend_Mut-WT" ftype="tabular" >
557 <assert_contents>
558 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
559 <has_text_matching expression="11304.*0.4540" />
560 </assert_contents>
561 </element>
467 </output_collection> 562 </output_collection>
468 </test> 563 </test>
469 </tests> 564 </tests>
470 565
471 <help><![CDATA[ 566 <help><![CDATA[
486 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most 581 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most
487 robust approach to differential expression is to use limma-trend. This approach will usually work well if the 582 robust approach to differential expression is to use limma-trend. This approach will usually work well if the
488 ratio of the largest library size to the smallest is not more than about 3-fold. When the library sizes are quite variable between samples, then the voom approach is theoretically more powerful than limma-trend. For more information see the excellent `limma User's Guide`_. 583 ratio of the largest library size to the smallest is not more than about 3-fold. When the library sizes are quite variable between samples, then the voom approach is theoretically more powerful than limma-trend. For more information see the excellent `limma User's Guide`_.
489 584
490 **Counts Data:** 585 **Counts Data:**
491
492 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 and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file. 586 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 and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
493 587
494 Example - **Separate Count Files**: 588 Example - **Separate Count Files**:
495 589
496 ========== ======= 590 ========== =======
518 ========== ======= ======= ======= ======== ======== ======== 612 ========== ======= ======= ======= ======== ======== ========
519 613
520 **Gene Annotations:** 614 **Gene Annotations:**
521 Optional input for gene annotations, this can contain more 615 Optional input for gene annotations, this can contain more
522 information about the genes than just an ID number. The annotations will 616 information about the genes than just an ID number. The annotations will
523 be available in the differential expression results table and the optional normalised counts table. 617 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
524 618
525 Example: 619 Example:
526 620
527 ========== ========== =================================================== 621 ========== ========== ===================================================
528 **GeneID** **Symbol** **GeneName** 622 **GeneID** **Symbol** **GeneName**
529 ---------- ---------- --------------------------------------------------- 623 ---------- ---------- ---------------------------------------------------
530 1287 Pzp pregnancy zone protein 624 11287 Pzp pregnancy zone protein
531 1298 Aanat arylalkylamine N-acetyltransferase 625 11298 Aanat arylalkylamine N-acetyltransferase
532 1302 Aatk apoptosis-associated tyrosine kinase 626 11302 Aatk apoptosis-associated tyrosine kinase
533 1303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 627 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
534 1304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4 628 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
535 1305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 629 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
536 ========== ========== =================================================== 630 ========== ========== ===================================================
537 631
538 **Factor Information:** 632 **Factor Information:**
539 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. 633 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.
540 634
553 647
554 *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. 648 *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.
555 649
556 *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. 650 *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.
557 651
558
559 **Gene Annotations:**
560 Optional input for gene annotations, this can contain more
561 information about the genes than just an ID number. The annotations will
562 be available in the differential expression results table and the optional normalised counts table.
563
564 Example:
565
566 ========== ========== ===================================================
567 **GeneID** **Symbol** **GeneName**
568 ---------- ---------- ---------------------------------------------------
569 1287 Pzp pregnancy zone protein
570 1298 Aanat arylalkylamine N-acetyltransferase
571 1302 Aatk apoptosis-associated tyrosine kinase
572 1303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
573 1304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
574 1305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
575 ========== ========== ===================================================
576 652
577 **Contrasts of Interest:** 653 **Contrasts of Interest:**
578 The contrasts you wish to make between levels. 654 The contrasts you wish to make between levels.
579 A common contrast would be a simple difference between two levels: "Mut-WT" 655 A common contrast would be a simple difference between two levels: "Mut-WT"
580 represents the difference between the mutant and wild type genotypes. 656 represents the difference between the mutant and wild type genotypes.
673 * a HTML report with plots and additional information 749 * a HTML report with plots and additional information
674 750
675 Optionally, under **Output Options** you can choose to output 751 Optionally, under **Output Options** you can choose to output
676 752
677 * a normalised counts table 753 * a normalised counts table
754 * the R script used by this tool
678 * an RData file 755 * an RData file
679 756
680 ----- 757 -----
681 758
682 **Citations:** 759 **Citations:**