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comparison limma_voom.xml @ 9:4255881bebb1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
author iuc
date Tue, 05 Jun 2018 04:28:56 -0400
parents 00a42b66e522
children e26047c4562d
comparison
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8:00a42b66e522 9:4255881bebb1
1 <tool id="limma_voom" name="limma" version="3.34.9.4"> 1 <tool id="limma_voom" name="limma" version="3.34.9.5">
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>
9 <requirement type="package" version="1.4.30">r-statmod</requirement> 9 <requirement type="package" version="1.4.30">r-statmod</requirement>
10 <requirement type="package" version="0.5.0">r-scales</requirement> 10 <requirement type="package" version="0.5.0">r-scales</requirement>
11 <requirement type="package" version="0.2.15">r-rjson</requirement> 11 <requirement type="package" version="0.2.15">r-rjson</requirement>
12 <requirement type="package" version="1.20.0">r-getopt</requirement> 12 <requirement type="package" version="1.20.0">r-getopt</requirement>
13 <requirement type="package" version="3.0.1">r-gplots</requirement> 13 <requirement type="package" version="3.0.1">r-gplots</requirement>
14 <requirement type="package" version="1.6.0">bioconductor-glimma</requirement>
14 </requirements> 15 </requirements>
15 16
16 <version_command><![CDATA[ 17 <version_command><![CDATA[
17 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 18 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
18 ]]></version_command> 19 ]]></version_command>
19 20
20 <command detect_errors="exit_code"><![CDATA[ 21 <command detect_errors="exit_code"><![CDATA[
21 #import json 22 #import json
22 Rscript '$__tool_directory__/limma_voom.R' 23 Rscript '$__tool_directory__/limma_voom.R'
108 109
109 && 110 &&
110 mkdir ./output_dir 111 mkdir ./output_dir
111 112
112 && 113 &&
113 cp '$outReport.files_path'/*.tsv output_dir/ 114 #if $anno.annoOpt=='yes':
115 cp -r ./glimma* '$outReport.files_path' &&
116 #end if
117 cp '$outReport.files_path'/*tsv output_dir/
114 118
115 #if $out.rscript: 119 #if $out.rscript:
116 && cp '$__tool_directory__/limma_voom.R' '$rscript' 120 && cp '$__tool_directory__/limma_voom.R' '$rscript'
117 #end if 121 #end if
118 ]]></command> 122 ]]></command>
192 </conditional> 196 </conditional>
193 197
194 <!-- Gene Annotations --> 198 <!-- Gene Annotations -->
195 <conditional name="anno"> 199 <conditional name="anno">
196 <param name="annoOpt" type="select" label="Use Gene Annotations?" 200 <param name="annoOpt" type="select" label="Use Gene Annotations?"
197 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene, and used to label the top genes in the Volcano plot. See Help section below."> 201 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene, and used to label the top genes in the Volcano plot. An interactive Glimma MD plot and table will also be generated. See Help section below.">
198 <option value="no">No</option> 202 <option value="no">No</option>
199 <option value="yes">Yes</option> 203 <option value="yes">Yes</option>
200 </param> 204 </param>
201 <when value="yes"> 205 <when value="yes">
202 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/> 206 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
395 <output name="outReport" > 399 <output name="outReport" >
396 <assert_contents> 400 <assert_contents>
397 <has_text text="RData" /> 401 <has_text text="RData" />
398 </assert_contents> 402 </assert_contents>
399 </output> 403 </output>
400 <output name="rscript" value="out_rscript.txt"/> 404 <output name="rscript">
405 <assert_contents>
406 <has_text_matching expression="Task run time" />
407 </assert_contents>
408 </output>
401 </test> 409 </test>
402 <!-- Ensure secondary factors work --> 410 <!-- Ensure secondary factors work -->
403 <test> 411 <test>
404 <param name="format" value="matrix" /> 412 <param name="format" value="matrix" />
405 <param name="counts" value="matrix.txt" /> 413 <param name="counts" value="matrix.txt" />
599 <help><![CDATA[ 607 <help><![CDATA[
600 .. class:: infomark 608 .. class:: infomark
601 609
602 **What it does** 610 **What it does**
603 611
604 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. 612 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. If an annotation file is provided, interactive Glimma_ plots and a table of differentially expressed genes will also be generated. See an example workflow here_.
605 613
606 In the `limma approach`_ to RNA-seq, read counts are converted to log2-counts-per-million (logCPM) and the mean-variance relationship is modelled either with precision weights or with an empirical Bayes prior trend. The precision weights approach is called “voom” and the prior trend approach is called “limma-trend”. For more information, see the Help section below. 614 In the `limma approach`_ to RNA-seq, read counts are converted to log2-counts-per-million (logCPM) and the mean-variance relationship is modelled either with precision weights or with an empirical Bayes prior trend. The precision weights approach is called “voom” and the prior trend approach is called “limma-trend”. For more information, see the Help section below.
607 615
608 ----- 616 -----
609 617
645 ========== ======= ======= ======= ======== ======== ======== 653 ========== ======= ======= ======= ======== ======== ========
646 654
647 **Gene Annotations:** 655 **Gene Annotations:**
648 Optional input for gene annotations, this can contain more 656 Optional input for gene annotations, this can contain more
649 information about the genes than just an ID number. The annotations will 657 information about the genes than just an ID number. The annotations will
650 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The second column will be used to label the genes in the Volcano plot instead of the default Gene IDs. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish. 658 be available in the differential expression results table and the optional normalised counts table. They will also be used to generate interactive Glimma_ MD plots and table of differential expression, a link to the Glimma plots will be provided in the report. The input annotation file must contain a header row and have the gene IDs in the first column. The second column will be used to label the genes in the Volcano plot and interactive Glimma plots, additional columns will be available in the Glimma interactive table. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
651 659
652 Example: 660 Example:
653 661
654 ========== ========== =================================================== 662 ========== ========== ===================================================
655 **GeneID** **Symbol** **GeneName** 663 **GeneID** **Symbol** **GeneName**
781 789
782 This tool outputs 790 This tool outputs
783 791
784 * a table of differentially expressed genes for each contrast of interest 792 * a table of differentially expressed genes for each contrast of interest
785 * a HTML report with plots and additional information 793 * a HTML report with plots and additional information
794 * an interactive Glimma MD plot and table (if annotation file provided)
786 795
787 Optionally, under **Output Options** you can choose to output 796 Optionally, under **Output Options** you can choose to output
788 797
789 * a normalised counts table 798 * a normalised counts table
790 * the R script used by this tool 799 * the R script used by this tool
842 Nucleic Acids Research 40, 4288-4297 851 Nucleic Acids Research 40, 4288-4297
843 852
844 Please report problems or suggestions to: su.s@wehi.edu.au 853 Please report problems or suggestions to: su.s@wehi.edu.au
845 854
846 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html 855 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
856 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
857 .. _here: https://f1000research.com/articles/5-1408/v2
847 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792 858 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
848 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf 859 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
849 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html 860 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
850 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf 861 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
851 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553 862 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553