Mercurial > repos > iuc > limma_voom

comparison limma_voom.xml @ 17:86b3df7db58b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
author iuc
date Mon, 18 Feb 2019 17:49:24 -0500
parents 5d903d528193
children 97e06a4c7c75
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16:5d903d528193 17:86b3df7db58b
1 <tool id="limma_voom" name="limma" version="3.38.3"> 1 <tool id="limma_voom" name="limma" version="3.38.3+galaxy1">
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>
160 <option value="matrix">Single Count Matrix</option> 160 <option value="matrix">Single Count Matrix</option>
161 </param> 161 </param>
162 162
163 <when value="files"> 163 <when value="files">
164 <repeat name="rep_factor" title="Factor" min="1"> 164 <repeat name="rep_factor" title="Factor" min="1">
165 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter"> 165 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
166 <sanitizer> 166 <sanitizer>
167 <valid initial="string.letters,string.digits"><add value="_" /></valid> 167 <valid initial="string.letters,string.digits"><add value="_" /></valid>
168 </sanitizer> 168 </sanitizer>
169 </param> 169 </param>
170 <repeat name="rep_group" title="Group" min="2" default="2"> 170 <repeat name="rep_group" title="Group" min="2" default="2">
171 <param name="groupName" type="text" label="Name" 171 <param name="groupName" type="text" label="Name"
172 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), and the first character of each group must be a letter"> 172 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).">
173 <sanitizer> 173 <sanitizer>
174 <valid initial="string.letters,string.digits"><add value="_" /></valid> 174 <valid initial="string.letters,string.digits"><add value="_" /></valid>
175 </sanitizer> 175 </sanitizer>
176 </param> 176 </param>
177 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/> 177 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
182 <when value="matrix"> 182 <when value="matrix">
183 <param name="counts" type="data" format="tabular" label="Count Matrix"/> 183 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
184 184
185 <conditional name="fact"> 185 <conditional name="fact">
186 <param name="ffile" type="select" label="Input factor information from file?" 186 <param name="ffile" type="select" label="Input factor information from file?"
187 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each sample, factor and group must be a letter"> 187 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
188 <option value="no">No</option> 188 <option value="no">No</option>
189 <option value="yes">Yes</option> 189 <option value="yes">Yes</option>
190 </param> 190 </param>
191 <when value="yes"> 191 <when value="yes">
192 <param name="finfo" type="data" format="tabular" label="Factor File"/> 192 <param name="finfo" type="data" format="tabular" label="Factor File"/>
193 </when> 193 </when>
194 <when value="no" > 194 <when value="no" >
195 <repeat name="rep_factor" title="Factor" min="1"> 195 <repeat name="rep_factor" title="Factor" min="1">
196 <param name="factorName" type="text" label="Factor Name" 196 <param name="factorName" type="text" label="Factor Name"
197 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter"> 197 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
198 <validator type="empty_field" /> 198 <validator type="empty_field" />
199 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator> 199 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
200 </param> 200 </param>
201 <param name="groupNames" type="text" label="Groups" 201 <param name="groupNames" type="text" label="Groups"
202 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter"> 202 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
203 <validator type="empty_field" /> 203 <validator type="empty_field" />
204 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator> 204 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
205 </param> 205 </param>
206 </repeat> 206 </repeat>
207 </when> 207 </when>
351 </data> 351 </data>
352 </outputs> 352 </outputs>
353 353
354 <tests> 354 <tests>
355 <!-- Ensure report is output --> 355 <!-- Ensure report is output -->
356 <test> 356 <test expect_num_outputs="2">
357 <param name="format" value="matrix" /> 357 <param name="format" value="matrix" />
358 <param name="counts" value="matrix.txt" /> 358 <param name="counts" value="matrix.txt" />
359 <repeat name="rep_factor"> 359 <repeat name="rep_factor">
360 <param name="factorName" value="Genotype"/> 360 <param name="factorName" value="Genotype"/>
361 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 361 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
389 <not_has_text text="RData" /> 389 <not_has_text text="RData" />
390 </assert_contents> 390 </assert_contents>
391 </output> 391 </output>
392 </test> 392 </test>
393 <!-- Ensure annotation file input works --> 393 <!-- Ensure annotation file input works -->
394 <test> 394 <test expect_num_outputs="2">
395 <param name="format" value="matrix" /> 395 <param name="format" value="matrix" />
396 <param name="annoOpt" value="yes" /> 396 <param name="annoOpt" value="yes" />
397 <param name="geneanno" value="anno.txt" /> 397 <param name="geneanno" value="anno.txt" />
398 <param name="counts" value="matrix.txt" /> 398 <param name="counts" value="matrix.txt" />
399 <repeat name="rep_factor"> 399 <repeat name="rep_factor">
413 </assert_contents> 413 </assert_contents>
414 </element> 414 </element>
415 </output_collection> 415 </output_collection>
416 </test> 416 </test>
417 <!-- Ensure Rscript and RData file can be output --> 417 <!-- Ensure Rscript and RData file can be output -->
418 <test> 418 <test expect_num_outputs="3">
419 <param name="format" value="matrix" /> 419 <param name="format" value="matrix" />
420 <param name="rscript" value="True"/> 420 <param name="rscript" value="True"/>
421 <param name="rdaOption" value="true" /> 421 <param name="rdaOption" value="true" />
422 <param name="counts" value="matrix.txt" /> 422 <param name="counts" value="matrix.txt" />
423 <repeat name="rep_factor"> 423 <repeat name="rep_factor">
439 <has_text_matching expression="Task run time" /> 439 <has_text_matching expression="Task run time" />
440 </assert_contents> 440 </assert_contents>
441 </output> 441 </output>
442 </test> 442 </test>
443 <!-- Ensure secondary factors work --> 443 <!-- Ensure secondary factors work -->
444 <test> 444 <test expect_num_outputs="2">
445 <param name="format" value="matrix" /> 445 <param name="format" value="matrix" />
446 <param name="counts" value="matrix.txt" /> 446 <param name="counts" value="matrix.txt" />
447 <repeat name="rep_factor"> 447 <repeat name="rep_factor">
448 <param name="factorName" value="Genotype"/> 448 <param name="factorName" value="Genotype"/>
449 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 449 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
465 </assert_contents> 465 </assert_contents>
466 </element> 466 </element>
467 </output_collection> 467 </output_collection>
468 </test> 468 </test>
469 <!-- Ensure factors file with unordered samples works --> 469 <!-- Ensure factors file with unordered samples works -->
470 <test> 470 <test expect_num_outputs="2">
471 <param name="format" value="matrix" /> 471 <param name="format" value="matrix" />
472 <param name="ffile" value="yes" /> 472 <param name="ffile" value="yes" />
473 <param name="finfo" value="factorinfo.txt" /> 473 <param name="finfo" value="factorinfo.txt" />
474 <param name="counts" value="matrix.txt" /> 474 <param name="counts" value="matrix.txt" />
475 <repeat name="rep_contrast"> 475 <repeat name="rep_contrast">
485 </assert_contents> 485 </assert_contents>
486 </element> 486 </element>
487 </output_collection> 487 </output_collection>
488 </test> 488 </test>
489 <!-- Ensure filtered and normalised count outputs works--> 489 <!-- Ensure filtered and normalised count outputs works-->
490 <test> 490 <test expect_num_outputs="4">
491 <param name="format" value="matrix" /> 491 <param name="format" value="matrix" />
492 <param name="filtCounts" value="true" /> 492 <param name="filtCounts" value="true" />
493 <param name="normCounts" value="true" /> 493 <param name="normCounts" value="true" />
494 <param name="counts" value="matrix.txt" /> 494 <param name="counts" value="matrix.txt" />
495 <repeat name="rep_factor"> 495 <repeat name="rep_factor">
527 <not_has_text text="11302"/> 527 <not_has_text text="11302"/>
528 </assert_contents> 528 </assert_contents>
529 </output> 529 </output>
530 </test> 530 </test>
531 <!-- Ensure multiple counts files input works --> 531 <!-- Ensure multiple counts files input works -->
532 <test> 532 <test expect_num_outputs="3">
533 <param name="format" value="files" /> 533 <param name="format" value="files" />
534 <repeat name="rep_factor"> 534 <repeat name="rep_factor">
535 <param name="factorName" value="Genotype"/> 535 <param name="factorName" value="Genotype"/>
536 <repeat name="rep_group"> 536 <repeat name="rep_group">
537 <param name="groupName" value="WT"/> 537 <param name="groupName" value="WT"/>
587 <has_text_matching expression="11304.*Abca4.*15.7545" /> 587 <has_text_matching expression="11304.*Abca4.*15.7545" />
588 </assert_contents> 588 </assert_contents>
589 </output> 589 </output>
590 </test> 590 </test>
591 <!-- Ensure limma-trend option works --> 591 <!-- Ensure limma-trend option works -->
592 <test> 592 <test expect_num_outputs="2">
593 <param name="format" value="matrix" /> 593 <param name="format" value="matrix" />
594 <param name="counts" value="matrix.txt" /> 594 <param name="counts" value="matrix.txt" />
595 <repeat name="rep_factor"> 595 <repeat name="rep_factor">
596 <param name="factorName" value="Genotype"/> 596 <param name="factorName" value="Genotype"/>
597 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 597 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
600 <param name="contrast" value="Mut-WT" /> 600 <param name="contrast" value="Mut-WT" />
601 </repeat> 601 </repeat>
602 <param name="normalisationOption" value="TMM" /> 602 <param name="normalisationOption" value="TMM" />
603 <param name="topgenes" value="6" /> 603 <param name="topgenes" value="6" />
604 <param name="de_select" value="trend" /> 604 <param name="de_select" value="trend" />
605 <param name="rdaOption" value="true" />
606 <output name="outReport" > 605 <output name="outReport" >
607 <assert_contents> 606 <assert_contents>
608 <has_text text="The limma-trend method was used" /> 607 <has_text text="The limma-trend method was used" />
609 </assert_contents> 608 </assert_contents>
610 </output> 609 </output>
616 </assert_contents> 615 </assert_contents>
617 </element> 616 </element>
618 </output_collection> 617 </output_collection>
619 </test> 618 </test>
620 <!-- Ensure limma-trend option with annotation works --> 619 <!-- Ensure limma-trend option with annotation works -->
621 <test> 620 <test expect_num_outputs="2">
622 <param name="format" value="matrix" /> 621 <param name="format" value="matrix" />
623 <param name="counts" value="matrix.txt" /> 622 <param name="counts" value="matrix.txt" />
624 <param name="annoOpt" value="yes" /> 623 <param name="annoOpt" value="yes" />
625 <param name="geneanno" value="anno.txt" /> 624 <param name="geneanno" value="anno.txt" />
626 <repeat name="rep_factor"> 625 <repeat name="rep_factor">
631 <param name="contrast" value="Mut-WT" /> 630 <param name="contrast" value="Mut-WT" />
632 </repeat> 631 </repeat>
633 <param name="normalisationOption" value="TMM" /> 632 <param name="normalisationOption" value="TMM" />
634 <param name="topgenes" value="6" /> 633 <param name="topgenes" value="6" />
635 <param name="de_select" value="trend" /> 634 <param name="de_select" value="trend" />
636 <param name="rdaOption" value="true" />
637 <output name="outReport" > 635 <output name="outReport" >
638 <assert_contents> 636 <assert_contents>
639 <has_text text="The limma-trend method was used" /> 637 <has_text text="The limma-trend method was used" />
640 </assert_contents> 638 </assert_contents>
641 </output> 639 </output>
646 <has_text_matching expression="11304.*0.4540" /> 644 <has_text_matching expression="11304.*0.4540" />
647 </assert_contents> 645 </assert_contents>
648 </element> 646 </element>
649 </output_collection> 647 </output_collection>
650 </test> 648 </test>
649 <!-- Ensure samples and groups beginning with numbers can be handled -->
650 <test expect_num_outputs="3">
651 <param name="format" value="matrix" />
652 <param name="counts" value="matrix_num.txt" />
653 <param name="annoOpt" value="yes" />
654 <param name="geneanno" value="anno.txt" />
655 <repeat name="rep_factor">
656 <param name="factorName" value="Group"/>
657 <param name="groupNames" value="2,2,2,1,1,1" />
658 </repeat>
659 <repeat name="rep_contrast">
660 <param name="contrast" value="2-1" />
661 </repeat>
662 <param name="filt_select" value="yes" />
663 <param name="format_select" value="counts"/>
664 <param name="cntReq" value="10"/>
665 <param name="count_select" value="sample"/>
666 <param name="cntSampleReq" value="3"/>
667 <param name="normalisationOption" value="TMM" />
668 <param name="normCounts" value="true" />
669 <param name="topgenes" value="6" />
670 <param name="de_select" value="voom" />
671 <output_collection name="outTables" count="1">
672 <element name="limma-voom_X2-X1" ftype="tabular" >
673 <assert_contents>
674 <has_text_matching expression="EntrezID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
675 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
676 </assert_contents>
677 </element>
678 </output_collection>
679 <output name="outNorm" ftype="tabular" >
680 <assert_contents>
681 <has_text_matching expression="EntrezID.*2-1.*2-2.*2-3.*1-1.*1-2.*1-3" />
682 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
683 </assert_contents>
684 </output>
685 </test>
651 </tests> 686 </tests>
652 687
653 <help><![CDATA[ 688 <help><![CDATA[
654 .. class:: infomark 689 .. class:: infomark
655 690
730 Mut1 Mut b1 765 Mut1 Mut b1
731 Mut2 Mut b2 766 Mut2 Mut b2
732 Mut3 Mut b3 767 Mut3 Mut b3
733 ========== ============ ========= 768 ========== ============ =========
734 769
735 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered, the name should start with a letter 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, an additive linear model will be used. 770 *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, an additive linear model will be used.
736 771
737 *Groups:* The names of the groups for the factor. The names should start with a letter, and only contain letters, numbers and underscores, other characters such as spaces and hyphens must not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. 772 *Groups:* The names of the groups for the factor. The names should only contain letters, numbers and underscores, other characters such as spaces and hyphens MUST not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. If the group names begin with a number an X will be added as a prefix.
738 773
739 **Contrasts of Interest:** 774 **Contrasts of Interest:**
740 The contrasts you wish to make between levels. 775 The contrasts you wish to make between levels.
741 A common contrast would be a simple difference between two levels: "Mut-WT" 776 A common contrast would be a simple difference between two levels: "Mut-WT"
742 represents the difference between the mutant and wild type genotypes. 777 represents the difference between the mutant and wild type genotypes.