Mercurial > repos > iuc > limma_voom

comparison limma_voom.xml @ 13:a984bbe87e2a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
author iuc
date Sun, 30 Sep 2018 10:51:12 -0400
parents 324417ddf9b9
children 94f82c79fa66
comparison
equal deleted inserted replaced
12:324417ddf9b9 13:a984bbe87e2a
1 <tool id="limma_voom" name="limma" version="3.34.9.8"> 1 <tool id="limma_voom" name="limma" version="3.34.9.9">
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>
121 121
122 && 122 &&
123 #if $anno.annoOpt=='yes': 123 #if $anno.annoOpt=='yes':
124 cp -r ./glimma* '$outReport.files_path' && 124 cp -r ./glimma* '$outReport.files_path' &&
125 #end if 125 #end if
126
126 cp '$outReport.files_path'/*tsv output_dir/ 127 cp '$outReport.files_path'/*tsv output_dir/
128
129 #if $out.filtCounts or $out.normCounts:
130 && cp '$outReport.files_path'/*counts output_dir/
131 #end if
127 132
128 #if $out.rscript: 133 #if $out.rscript:
129 && cp '$__tool_directory__/limma_voom.R' '$rscript' 134 && cp '$__tool_directory__/limma_voom.R' '$rscript'
130 #end if 135 #end if
131 ]]></command> 136 ]]></command>
326 331
327 </inputs> 332 </inputs>
328 333
329 <outputs> 334 <outputs>
330 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" /> 335 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
331 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> 336 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables">
332 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> 337 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
333 </collection> 338 </collection>
339 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts">
340 <filter>out['filtCounts']</filter>
341 </data>
342 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts">
343 <filter>out['normCounts']</filter>
344 </data>
334 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> 345 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
335 <filter>out['rscript']</filter> 346 <filter>out['rscript']</filter>
336 </data> 347 </data>
337 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information"> 348 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
338 <filter>out['libinfo']</filter> 349 <filter>out['libinfo']</filter>
491 <param name="cntReq" value="10"/> 502 <param name="cntReq" value="10"/>
492 <param name="count_select" value="sample"/> 503 <param name="count_select" value="sample"/>
493 <param name="cntSampleReq" value="3"/> 504 <param name="cntSampleReq" value="3"/>
494 <param name="normalisationOption" value="TMM" /> 505 <param name="normalisationOption" value="TMM" />
495 <param name="topgenes" value="6" /> 506 <param name="topgenes" value="6" />
496 <output_collection name="outTables" count="3"> 507 <output_collection name="outTables" count="1">
497 <element name="limma-voom_Mut-WT" ftype="tabular" > 508 <element name="limma-voom_Mut-WT" ftype="tabular" >
498 <assert_contents> 509 <assert_contents>
499 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> 510 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
500 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" /> 511 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
501 </assert_contents> 512 </assert_contents>
502 </element> 513 </element>
503 <element name="limma-voom_normcounts" ftype="tabular" >
504 <assert_contents>
505 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
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"/>
514 </assert_contents>
515 </element>
516 </output_collection> 514 </output_collection>
515 <output name="outNorm" ftype="tabular" >
516 <assert_contents>
517 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
518 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
519 </assert_contents>
520 </output>
521 <output name="outFilt" ftype="tabular" >
522 <assert_contents>
523 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
524 <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" />
525 <not_has_text text="11302"/>
526 </assert_contents>
527 </output>
517 </test> 528 </test>
518 <!-- Ensure multiple counts files input works --> 529 <!-- Ensure multiple counts files input works -->
519 <test> 530 <test>
520 <param name="format" value="files" /> 531 <param name="format" value="files" />
521 <repeat name="rep_factor"> 532 <repeat name="rep_factor">
552 <repeat name="rep_contrast"> 563 <repeat name="rep_contrast">
553 <param name="contrast" value="WT-Mut" /> 564 <param name="contrast" value="WT-Mut" />
554 </repeat> 565 </repeat>
555 <param name="topgenes" value="6" /> 566 <param name="topgenes" value="6" />
556 <param name="normCounts" value="true" /> 567 <param name="normCounts" value="true" />
557 <output_collection name="outTables" count="3"> 568 <output_collection name="outTables" count="2">
558 <element name="limma-voom_Mut-WT" ftype="tabular" > 569 <element name="limma-voom_Mut-WT" ftype="tabular" >
559 <assert_contents> 570 <assert_contents>
560 <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> 571 <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
561 <has_text_matching expression="11304.*Abca4.*0.4590" /> 572 <has_text_matching expression="11304.*Abca4.*0.4590" />
562 </assert_contents> 573 </assert_contents>
565 <assert_contents> 576 <assert_contents>
566 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> 577 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
567 <has_text_matching expression="11304.*Abca4.*-0.4590" /> 578 <has_text_matching expression="11304.*Abca4.*-0.4590" />
568 </assert_contents> 579 </assert_contents>
569 </element> 580 </element>
570 <element name="limma-voom_normcounts" ftype="tabular" >
571 <assert_contents>
572 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
573 <has_text_matching expression="11304.*Abca4.*15.7545" />
574 </assert_contents>
575 </element>
576 </output_collection> 581 </output_collection>
582 <output name="outNorm" ftype="tabular" >
583 <assert_contents>
584 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
585 <has_text_matching expression="11304.*Abca4.*15.7545" />
586 </assert_contents>
587 </output>
577 </test> 588 </test>
578 <!-- Ensure limma-trend option works --> 589 <!-- Ensure limma-trend option works -->
579 <test> 590 <test>
580 <param name="format" value="matrix" /> 591 <param name="format" value="matrix" />
581 <param name="counts" value="matrix.txt" /> 592 <param name="counts" value="matrix.txt" />