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comparison deseq2.xml @ 29:cd9874cb9019 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
author iuc
date Mon, 29 Nov 2021 18:16:48 +0000
parents 7ff33c2d525b
children 8fe98f7094de
comparison
equal deleted inserted replaced
28:7ff33c2d525b 29:cd9874cb9019
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&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/> 219 <discover_datasets pattern="(?P&lt;designation&gt;.+_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>