Mercurial > repos > iuc > deseq2
comparison deseq2.xml @ 29:cd9874cb9019 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
author | iuc |
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date | Mon, 29 Nov 2021 18:16:48 +0000 |
parents | 7ff33c2d525b |
children | 8fe98f7094de |
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28:7ff33c2d525b | 29:cd9874cb9019 |
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44 -p '$plots' | 44 -p '$plots' |
45 #end if | 45 #end if |
46 -A $output_options.alpha_ma | 46 -A $output_options.alpha_ma |
47 #if 'normCounts' in $output_options.output_selector: | 47 #if 'normCounts' in $output_options.output_selector: |
48 -n '$counts_out' | 48 -n '$counts_out' |
49 #end if | |
50 #if 'sizefactors' in $output_options.output_selector: | |
51 -F '$sizefactors_out' | |
49 #end if | 52 #end if |
50 #if 'normRLog' in $output_options.output_selector: | 53 #if 'normRLog' in $output_options.output_selector: |
51 -r '$rlog_out' | 54 -r '$rlog_out' |
52 #end if | 55 #end if |
53 #if 'normVST' in $output_options.output_selector: | 56 #if 'normVST' in $output_options.output_selector: |
193 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> | 196 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> |
194 </section> | 197 </section> |
195 <section name="output_options" title="Output options"> | 198 <section name="output_options" title="Output options"> |
196 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector"> | 199 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector"> |
197 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option> | 200 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option> |
201 <option value="sizefactors" >Output sample size factors</option> | |
198 <option value="normCounts">Output normalised counts</option> | 202 <option value="normCounts">Output normalised counts</option> |
199 <option value="normVST">Output VST normalized table</option> | 203 <option value="normVST">Output VST normalized table</option> |
200 <option value="normRLog">Output rLog normalized table</option> | 204 <option value="normRLog">Output rLog normalized table</option> |
201 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option> | 205 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option> |
202 </param> | 206 </param> |
215 <discover_datasets pattern="(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> | 219 <discover_datasets pattern="(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> |
216 </collection> | 220 </collection> |
217 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> | 221 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> |
218 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter> | 222 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter> |
219 </data> | 223 </data> |
224 <data name="sizefactors_out" format="tabular" label="Size Factors on ${on_string}"> | |
225 <filter>output_options['output_selector'] and 'sizefactors' in output_options['output_selector']</filter> | |
226 </data> | |
220 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}"> | 227 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}"> |
221 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter> | 228 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter> |
222 </data> | 229 </data> |
223 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}"> | 230 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}"> |
224 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter> | 231 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter> |
511 <assert_contents> | 518 <assert_contents> |
512 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" /> | 519 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" /> |
513 </assert_contents> | 520 </assert_contents> |
514 </output> | 521 </output> |
515 </test> | 522 </test> |
523 <!-- Same as above alpha_ma test, but with size factors --> | |
524 <test expect_num_outputs="2"> | |
525 <repeat name="rep_factorName"> | |
526 <param name="factorName" value="Treatment"/> | |
527 <repeat name="rep_factorLevel"> | |
528 <param name="factorLevel" value="Treated"/> | |
529 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> | |
530 </repeat> | |
531 <repeat name="rep_factorLevel"> | |
532 <param name="factorLevel" value="Untreated"/> | |
533 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> | |
534 </repeat> | |
535 </repeat> | |
536 <section name="output_options"> | |
537 <param name="output_selector" value="sizefactors"/> | |
538 <param name="alpha_ma" value="0.05"/> | |
539 </section> | |
540 <param name="tximport_selector" value="tximport"/> | |
541 <param name="txtype" value="sailfish"/> | |
542 <param name="mapping_format_selector" value="gtf"/> | |
543 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> | |
544 <output name="sizefactors_out"> | |
545 <assert_contents> | |
546 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" /> | |
547 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" /> | |
548 </assert_contents> | |
549 </output> | |
550 </test> | |
551 <!-- Same as above alpha_ma size factor test, but with a non-default estimator--> | |
552 <test expect_num_outputs="2"> | |
553 <repeat name="rep_factorName"> | |
554 <param name="factorName" value="Treatment"/> | |
555 <repeat name="rep_factorLevel"> | |
556 <param name="factorLevel" value="Treated"/> | |
557 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> | |
558 </repeat> | |
559 <repeat name="rep_factorLevel"> | |
560 <param name="factorLevel" value="Untreated"/> | |
561 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> | |
562 </repeat> | |
563 </repeat> | |
564 <section name="advanced_options"> | |
565 <param name="esf" value="poscounts" /> | |
566 </section> | |
567 <section name="output_options"> | |
568 <param name="output_selector" value="sizefactors"/> | |
569 <param name="alpha_ma" value="0.05"/> | |
570 </section> | |
571 <param name="tximport_selector" value="tximport"/> | |
572 <param name="txtype" value="sailfish"/> | |
573 <param name="mapping_format_selector" value="gtf"/> | |
574 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> | |
575 <output name="sizefactors_out" > | |
576 <assert_contents> | |
577 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" /> | |
578 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" /> | |
579 </assert_contents> | |
580 </output> | |
581 </test> | |
516 </tests> | 582 </tests> |
517 <help><![CDATA[ | 583 <help><![CDATA[ |
518 .. class:: infomark | 584 .. class:: infomark |
519 | 585 |
520 **What it does** | 586 **What it does** |
606 6 p value for the statistical significance of this change | 672 6 p value for the statistical significance of this change |
607 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure | 673 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure |
608 which controls false discovery rate (FDR) | 674 which controls false discovery rate (FDR) |
609 ====== ========================================================== | 675 ====== ========================================================== |
610 | 676 |
677 By selecting ``Output sample size factors`` in the "Output options" | |
678 selection box, the size factors used to normalize the samples can also | |
679 be output as a tabular file. | |
680 | |
611 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html | 681 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html |
612 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html | 682 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html |
613 ]]></help> | 683 ]]></help> |
614 <expand macro="citations" /> | 684 <expand macro="citations" /> |
615 </tool> | 685 </tool> |