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comparison limma_voom.xml @ 19:04cb660cbf5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
author iuc
date Tue, 28 May 2019 10:03:49 -0400
parents be6802c62dfc
children 455d6445a6a0
comparison
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18:be6802c62dfc 19:04cb660cbf5d
1 <tool id="limma_voom" name="limma" version="3.38.3+galaxy2"> 1 <tool id="limma_voom" name="limma" version="3.38.3+galaxy3">
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>
55 55
56 #if $anno.annoOpt=='yes': 56 #if $anno.annoOpt=='yes':
57 -a '$anno.geneanno' 57 -a '$anno.geneanno'
58 #end if 58 #end if
59 59
60 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }' 60 #if $cont.cfile=='yes':
61 -C '$cont.cinfo'
62 #else:
63 -D '${ ','.join( ['%s' % $x.contrast for x in $cont.rep_contrast] ) }'
64 #end if
61 65
62 #if $f.filt.filt_select == 'yes': 66 #if $f.filt.filt_select == 'yes':
63 #if $f.filt.cformat.format_select == 'cpm': 67 #if $f.filt.cformat.format_select == 'cpm':
64 -c '$f.filt.cformat.cpmReq' 68 -c '$f.filt.cformat.cpmReq'
65 -s '$f.filt.cformat.cpmSampleReq' 69 -s '$f.filt.cformat.cpmSampleReq'
221 </when> 225 </when>
222 <when value="no" /> 226 <when value="no" />
223 </conditional> 227 </conditional>
224 228
225 <!-- Contrasts --> 229 <!-- Contrasts -->
226 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> 230 <conditional name="cont">
227 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> 231 <param name="cfile" type="select" label="Input Contrast information from file?"
228 <validator type="empty_field" /> 232 help="You can choose to input the contrast 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. Use a hyphen to separate the groups you want to compare, as shown in the Help section below.">
229 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator> 233 <option value="no">No</option>
234 <option value="yes">Yes</option>
230 </param> 235 </param>
231 </repeat> 236 <when value="yes">
237 <param name="cinfo" type="data" format="tabular" label="Contrasts File"/>
238 </when>
239 <when value="no" >
240 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
241 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
242 <validator type="empty_field" />
243 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
244 </param>
245 </repeat>
246 </when>
247 </conditional>
232 248
233 <!-- Filter Options --> 249 <!-- Filter Options -->
234 <section name="f" expanded="false" title="Filter Low Counts"> 250 <section name="f" expanded="false" title="Filter Low Counts">
235 <conditional name="filt"> 251 <conditional name="filt">
236 <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No"> 252 <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No">
358 <param name="counts" value="matrix.txt" /> 374 <param name="counts" value="matrix.txt" />
359 <repeat name="rep_factor"> 375 <repeat name="rep_factor">
360 <param name="factorName" value="Genotype"/> 376 <param name="factorName" value="Genotype"/>
361 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 377 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
362 </repeat> 378 </repeat>
379 <param name="cfile" value="no" />
363 <repeat name="rep_contrast"> 380 <repeat name="rep_contrast">
364 <param name="contrast" value="Mut-WT" /> 381 <param name="contrast" value="Mut-WT" />
365 </repeat> 382 </repeat>
366 <repeat name="rep_contrast"> 383 <repeat name="rep_contrast">
367 <param name="contrast" value="WT-Mut" /> 384 <param name="contrast" value="WT-Mut" />
398 <param name="counts" value="matrix.txt" /> 415 <param name="counts" value="matrix.txt" />
399 <repeat name="rep_factor"> 416 <repeat name="rep_factor">
400 <param name="factorName" value="Genotype"/> 417 <param name="factorName" value="Genotype"/>
401 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 418 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
402 </repeat> 419 </repeat>
420 <param name="cfile" value="no" />
403 <repeat name="rep_contrast"> 421 <repeat name="rep_contrast">
404 <param name="contrast" value="Mut-WT" /> 422 <param name="contrast" value="Mut-WT" />
405 </repeat> 423 </repeat>
406 <param name="normalisationOption" value="TMM" /> 424 <param name="normalisationOption" value="TMM" />
407 <param name="topgenes" value="6" /> 425 <param name="topgenes" value="6" />
422 <param name="counts" value="matrix.txt" /> 440 <param name="counts" value="matrix.txt" />
423 <repeat name="rep_factor"> 441 <repeat name="rep_factor">
424 <param name="factorName" value="Genotype"/> 442 <param name="factorName" value="Genotype"/>
425 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 443 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
426 </repeat> 444 </repeat>
445 <param name="cfile" value="no" />
427 <repeat name="rep_contrast"> 446 <repeat name="rep_contrast">
428 <param name="contrast" value="Mut-WT" /> 447 <param name="contrast" value="Mut-WT" />
429 </repeat> 448 </repeat>
430 <param name="normalisationOption" value="TMM" /> 449 <param name="normalisationOption" value="TMM" />
431 <param name="topgenes" value="6" /> 450 <param name="topgenes" value="6" />
450 </repeat> 469 </repeat>
451 <repeat name="rep_factor"> 470 <repeat name="rep_factor">
452 <param name="factorName" value="Batch"/> 471 <param name="factorName" value="Batch"/>
453 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/> 472 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
454 </repeat> 473 </repeat>
474 <param name="cfile" value="no" />
455 <repeat name="rep_contrast"> 475 <repeat name="rep_contrast">
456 <param name="contrast" value="Mut-WT" /> 476 <param name="contrast" value="Mut-WT" />
457 </repeat> 477 </repeat>
458 <param name="normalisationOption" value="TMM" /> 478 <param name="normalisationOption" value="TMM" />
459 <param name="topgenes" value="6" /> 479 <param name="topgenes" value="6" />
470 <test expect_num_outputs="2"> 490 <test expect_num_outputs="2">
471 <param name="format" value="matrix" /> 491 <param name="format" value="matrix" />
472 <param name="ffile" value="yes" /> 492 <param name="ffile" value="yes" />
473 <param name="finfo" value="factorinfo.txt" /> 493 <param name="finfo" value="factorinfo.txt" />
474 <param name="counts" value="matrix.txt" /> 494 <param name="counts" value="matrix.txt" />
495 <param name="cfile" value="no" />
475 <repeat name="rep_contrast"> 496 <repeat name="rep_contrast">
476 <param name="contrast" value="Mut-WT" /> 497 <param name="contrast" value="Mut-WT" />
477 </repeat> 498 </repeat>
478 <param name="normalisationOption" value="TMM" /> 499 <param name="normalisationOption" value="TMM" />
479 <param name="topgenes" value="6" /> 500 <param name="topgenes" value="6" />
494 <param name="counts" value="matrix.txt" /> 515 <param name="counts" value="matrix.txt" />
495 <repeat name="rep_factor"> 516 <repeat name="rep_factor">
496 <param name="factorName" value="Genotype"/> 517 <param name="factorName" value="Genotype"/>
497 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 518 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
498 </repeat> 519 </repeat>
520 <param name="cfile" value="no" />
499 <repeat name="rep_contrast"> 521 <repeat name="rep_contrast">
500 <param name="contrast" value="Mut-WT" /> 522 <param name="contrast" value="Mut-WT" />
501 </repeat> 523 </repeat>
502 <param name="filt_select" value="yes" /> 524 <param name="filt_select" value="yes" />
503 <param name="format_select" value="counts"/> 525 <param name="format_select" value="counts"/>
557 <param name="countsFile" value="WT3.counts,Mut3.counts"/> 579 <param name="countsFile" value="WT3.counts,Mut3.counts"/>
558 </repeat> 580 </repeat>
559 </repeat> 581 </repeat>
560 <param name="annoOpt" value="yes" /> 582 <param name="annoOpt" value="yes" />
561 <param name="geneanno" value="anno.txt" /> 583 <param name="geneanno" value="anno.txt" />
584 <param name="cfile" value="no" />
562 <repeat name="rep_contrast"> 585 <repeat name="rep_contrast">
563 <param name="contrast" value="Mut-WT" /> 586 <param name="contrast" value="Mut-WT" />
564 </repeat> 587 </repeat>
565 <repeat name="rep_contrast"> 588 <repeat name="rep_contrast">
566 <param name="contrast" value="WT-Mut" /> 589 <param name="contrast" value="WT-Mut" />
594 <param name="counts" value="matrix.txt" /> 617 <param name="counts" value="matrix.txt" />
595 <repeat name="rep_factor"> 618 <repeat name="rep_factor">
596 <param name="factorName" value="Genotype"/> 619 <param name="factorName" value="Genotype"/>
597 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 620 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
598 </repeat> 621 </repeat>
622 <param name="cfile" value="no" />
599 <repeat name="rep_contrast"> 623 <repeat name="rep_contrast">
600 <param name="contrast" value="Mut-WT" /> 624 <param name="contrast" value="Mut-WT" />
601 </repeat> 625 </repeat>
602 <param name="normalisationOption" value="TMM" /> 626 <param name="normalisationOption" value="TMM" />
603 <param name="topgenes" value="6" /> 627 <param name="topgenes" value="6" />
624 <param name="geneanno" value="anno.txt" /> 648 <param name="geneanno" value="anno.txt" />
625 <repeat name="rep_factor"> 649 <repeat name="rep_factor">
626 <param name="factorName" value="Genotype"/> 650 <param name="factorName" value="Genotype"/>
627 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 651 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
628 </repeat> 652 </repeat>
653 <param name="cfile" value="no" />
629 <repeat name="rep_contrast"> 654 <repeat name="rep_contrast">
630 <param name="contrast" value="Mut-WT" /> 655 <param name="contrast" value="Mut-WT" />
631 </repeat> 656 </repeat>
632 <param name="normalisationOption" value="TMM" /> 657 <param name="normalisationOption" value="TMM" />
633 <param name="topgenes" value="6" /> 658 <param name="topgenes" value="6" />
654 <param name="geneanno" value="anno.txt" /> 679 <param name="geneanno" value="anno.txt" />
655 <repeat name="rep_factor"> 680 <repeat name="rep_factor">
656 <param name="factorName" value="Group"/> 681 <param name="factorName" value="Group"/>
657 <param name="groupNames" value="2,2,2,1,1,1" /> 682 <param name="groupNames" value="2,2,2,1,1,1" />
658 </repeat> 683 </repeat>
684 <param name="cfile" value="no" />
659 <repeat name="rep_contrast"> 685 <repeat name="rep_contrast">
660 <param name="contrast" value="2-1" /> 686 <param name="contrast" value="2-1" />
661 </repeat> 687 </repeat>
662 <param name="filt_select" value="yes" /> 688 <param name="filt_select" value="yes" />
663 <param name="format_select" value="counts"/> 689 <param name="format_select" value="counts"/>
681 <has_text_matching expression="EntrezID.*2-1.*2-2.*2-3.*1-1.*1-2.*1-3" /> 707 <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" /> 708 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
683 </assert_contents> 709 </assert_contents>
684 </output> 710 </output>
685 </test> 711 </test>
712 <!-- Ensure contrasts file works -->
713 <test expect_num_outputs="2">
714 <param name="format" value="matrix" />
715 <param name="counts" value="matrix.txt" />
716 <repeat name="rep_factor">
717 <param name="factorName" value="Genotype"/>
718 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
719 </repeat>
720 <param name="cfile" value="yes" />
721 <param name="cinfo" value="contrasts.txt" />
722 <param name="normalisationOption" value="TMM" />
723 <param name="topgenes" value="6" />
724 <output_collection name="outTables" count="2">
725 <element name="limma-voom_Mut-WT" ftype="tabular" >
726 <assert_contents>
727 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
728 <has_text_matching expression="11304.*0.4573" />
729 </assert_contents>
730 </element>
731 <element name="limma-voom_WT-Mut" ftype="tabular" >
732 <assert_contents>
733 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
734 <has_text_matching expression="11304.*-0.4573" />
735 </assert_contents>
736 </element>
737 </output_collection>
738 </test>
686 </tests> 739 </tests>
687 740
688 <help><![CDATA[ 741 <help><![CDATA[
689 .. class:: infomark 742 .. class:: infomark
690 743
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. 823 *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.
771 824
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. 825 *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.
773 826
774 **Contrasts of Interest:** 827 **Contrasts of Interest:**
775 The contrasts you wish to make between levels. 828 The contrasts you wish to make between levels. 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" 829 represents the difference between the mutant and wild type genotypes. Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. Alternatively, a tab-separated file can be input that has the names of the comparisons in the first column and one header row, as shown below.
777 represents the difference between the mutant and wild type genotypes. 830
778 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. 831 Example:
832
833 ============= =
834 **Contrasts**
835 ------------- -
836 Mut-WT
837 WT-Mut
838 ============= =
779 839
780 **Filter Low Counts:** 840 **Filter Low Counts:**
781 Genes with very low counts across all libraries provide little evidence for differential expression. 841 Genes with very low counts across all libraries provide little evidence for differential expression.
782 In the biological point of view, a gene must be expressed at some minimal level before 842 In the biological point of view, a gene must be expressed at some minimal level before
783 it is likely to be translated into a protein or to be biologically important. In addition, the 843 it is likely to be translated into a protein or to be biologically important. In addition, the