Mercurial > repos > iuc > limma_voom

comparison limma_voom.xml @ 12:324417ddf9b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
author iuc
date Sun, 05 Aug 2018 05:12:57 -0400
parents 0433416377de
children a984bbe87e2a
comparison
equal deleted inserted replaced
11:0433416377de 12:324417ddf9b9
1 <tool id="limma_voom" name="limma" version="3.34.9.7"> 1 <tool id="limma_voom" name="limma" version="3.34.9.8">
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>
73 #end if 73 #end if
74 #end if 74 #end if
75 75
76 #if $out.plots: 76 #if $out.plots:
77 -P $out.plots 77 -P $out.plots
78 #end if
79
80 #if $out.filtCounts:
81 -F
78 #end if 82 #end if
79 83
80 #if $out.normCounts: 84 #if $out.normCounts:
81 -x 85 -x
82 #end if 86 #end if
270 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option> 274 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
271 <option value="m">MD Plots for individual samples</option> 275 <option value="m">MD Plots for individual samples</option>
272 <option value="h">Heatmaps (top DE genes) </option> 276 <option value="h">Heatmaps (top DE genes) </option>
273 <option value="s">Stripcharts (top DE genes)</option> 277 <option value="s">Stripcharts (top DE genes)</option>
274 </param> 278 </param>
279 <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
280 label="Output Filtered Counts Table?"
281 help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
282 </param>
275 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 283 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
276 label="Output Normalised Counts Table?" 284 label="Output Normalised Counts Table?"
277 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> 285 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
278 </param> 286 </param>
279 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false" 287 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
463 <has_text_matching expression="11304.*0.4590" /> 471 <has_text_matching expression="11304.*0.4590" />
464 </assert_contents> 472 </assert_contents>
465 </element> 473 </element>
466 </output_collection> 474 </output_collection>
467 </test> 475 </test>
468 <!-- Ensure normalised counts file output works--> 476 <!-- Ensure filtered and normalised count outputs works-->
469 <test> 477 <test>
470 <param name="format" value="matrix" /> 478 <param name="format" value="matrix" />
479 <param name="filtCounts" value="true" />
471 <param name="normCounts" value="true" /> 480 <param name="normCounts" value="true" />
472 <param name="counts" value="matrix.txt" /> 481 <param name="counts" value="matrix.txt" />
473 <repeat name="rep_factor"> 482 <repeat name="rep_factor">
474 <param name="factorName" value="Genotype"/> 483 <param name="factorName" value="Genotype"/>
475 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> 484 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
476 </repeat> 485 </repeat>
477 <repeat name="rep_contrast"> 486 <repeat name="rep_contrast">
478 <param name="contrast" value="Mut-WT" /> 487 <param name="contrast" value="Mut-WT" />
479 </repeat> 488 </repeat>
489 <param name="filt_select" value="yes" />
490 <param name="format_select" value="counts"/>
491 <param name="cntReq" value="10"/>
492 <param name="count_select" value="sample"/>
493 <param name="cntSampleReq" value="3"/>
480 <param name="normalisationOption" value="TMM" /> 494 <param name="normalisationOption" value="TMM" />
481 <param name="topgenes" value="6" /> 495 <param name="topgenes" value="6" />
482 <output_collection name="outTables" count="2"> 496 <output_collection name="outTables" count="3">
483 <element name="limma-voom_Mut-WT" ftype="tabular" > 497 <element name="limma-voom_Mut-WT" ftype="tabular" >
484 <assert_contents> 498 <assert_contents>
485 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> 499 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
486 <has_text_matching expression="11304.*0.4573" /> 500 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
487 </assert_contents> 501 </assert_contents>
488 </element> 502 </element>
489 <element name="limma-voom_normcounts" ftype="tabular" > 503 <element name="limma-voom_normcounts" ftype="tabular" >
490 <assert_contents> 504 <assert_contents>
491 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> 505 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
492 <has_text_matching expression="11304.*15.7545" /> 506 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
507 </assert_contents>
508 </element>
509 <element name="limma-voom_filtcounts" ftype="tabular" >
510 <assert_contents>
511 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
512 <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" />
513 <not_has_text text="11302"/>
493 </assert_contents> 514 </assert_contents>
494 </element> 515 </element>
495 </output_collection> 516 </output_collection>
496 </test> 517 </test>
497 <!-- Ensure multiple counts files input works --> 518 <!-- Ensure multiple counts files input works -->