limma_voom: limma_voom.xml annotate

annotate limma_voom.xml @ 9:a30e66a28451 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0

author	iuc
date	Tue, 05 Jun 2018 04:28:39 -0400
parents	87f26da8078e
children	009d442415b7

rev	line source
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	1 <tool id="limma_voom" name="limma" version="3.34.9.5">
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	2 <description>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	3 Perform differential expression with limma-voom or limma-trend
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	4 </description>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	5
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	6 <requirements>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	7 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	9 <requirement type="package" version="1.4.30">r-statmod</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	10 <requirement type="package" version="0.5.0">r-scales</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	11 <requirement type="package" version="0.2.15">r-rjson</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	12 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	13 <requirement type="package" version="3.0.1">r-gplots</requirement>
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	14 <requirement type="package" version="1.6.0">bioconductor-glimma</requirement>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	15 </requirements>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	16
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	17 <version_command><![CDATA[
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	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" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	19 ]]></version_command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	20
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	21 <command detect_errors="exit_code"><![CDATA[
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	22 #import json
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	23 Rscript '$__tool_directory__/limma_voom.R'
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	24
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	25 -R '$outReport'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	26 -o '$outReport.files_path'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	27
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	28 #if $input.format=="files":
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	29
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	30 ## Adapted from DESeq2 wrapper
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	31 #set $temp_factor_names = list()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	32 #for $fact in $input.rep_factor:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	33 #set $temp_factor = list()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	34 #for $g in $fact.rep_group:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	35 #set $count_files = list()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	36 #for $file in $g.countsFile:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	37 $count_files.append(str($file))
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	38 #end for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	39 $temp_factor.append( {str($g.groupName): $count_files} )
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	40 #end for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	41
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	42 $temp_factor.reverse()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	43 $temp_factor_names.append([str($fact.factorName), $temp_factor])
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	44 #end for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	45 -j '#echo json.dumps(temp_factor_names)#'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	46
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	47 #elif $input.format=="matrix":
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	48 -m '$input.counts'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	49 #if $input.fact.ffile=='yes':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	50 -f '$input.fact.finfo'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	51 #else:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	52 -i '${ '\|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	53 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	54 #end if
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	55
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	56 #if $anno.annoOpt=='yes':
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	57 -a '$anno.geneanno'
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	58 #end if
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	59
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	60 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	61
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	62 #if $f.filt.filt_select == 'yes':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	63 #if $f.filt.cformat.format_select == 'cpm':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	64 -c '$f.filt.cformat.cpmReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	65 -s '$f.filt.cformat.cpmSampleReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	66 #elif $f.filt.cformat.format_select == 'counts':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	67 -z '$f.filt.cformat.cntReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	68 #if $f.filt.cformat.samples.count_select == 'total':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	69 -y
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	70 #elif $f.filt.cformat.samples.count_select == 'sample':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	71 -s '$f.filt.cformat.samples.cntSampleReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	72 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	73 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	74 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	75
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	76 #if $out.plots:
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	77 -P $out.plots
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	78 #end if
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	79
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	80 #if $out.normCounts:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	81 -x
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	82 #end if
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	83
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	84 #if $out.rdaOption:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	85 -r
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	86 #end if
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	87
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	88 -l '$adv.lfc'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	89 -p '$adv.pVal'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	90 -d '$adv.pAdjust'
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	91 -G '$adv.topgenes'
6 6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	92 #if $adv.treat:
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	93 -T
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	94 #end if
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	95
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	96 #if $deMethod.de_select == 'voom':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	97 #if $deMethod.weightOption:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	98 -w
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	99 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	100 #elif $deMethod.de_select == 'trend':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	101 -t $deMethod.prior_count
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	102 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	103
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	104 -n '$adv.normalisationOption'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	105
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	106 #if $adv.robOption:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	107 -b
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	108 #end if
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	109
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	110 &&
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	111 mkdir ./output_dir
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	112
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	113 &&
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	114 #if $anno.annoOpt=='yes':
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	115 cp -r ./glimma* '$outReport.files_path' &&
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	116 #end if
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	117 cp '$outReport.files_path'/*tsv output_dir/
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	118
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	119 #if $out.rscript:
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	120 && cp '$__tool_directory__/limma_voom.R' '$rscript'
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	121 #end if
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	122 ]]></command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	123
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	124 <inputs>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	125
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	126 <!-- DE Method Option -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	127 <conditional name="deMethod">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	128 <param name="de_select" type="select" label="Differential Expression Method" help="Select the limma-voom or limma-trend method. See Help section below for more information. Default: limma-voom">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	129 <option value="voom" selected="True">limma-voom</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	130 <option value="trend">limma-trend</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	131 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	132 <when value="voom">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	133 <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality weights?"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	134 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	135 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	136 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	137 <when value="trend">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	138 <param name="prior_count" type="float" min="0" value="3" label="Prior count" help="Average count to be added to each observation to avoid taking log of zero. Default: 3." />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	139 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	140 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	141 <!-- Counts and Factors -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	142 <conditional name="input">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	143 <param name="format" type="select" label="Count Files or Matrix?"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	144 help="You can choose to input either separate count files (one per sample) or a single count matrix">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	145 <option value="files">Separate Count Files</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	146 <option value="matrix">Single Count Matrix</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	147 </param>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	148
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	149 <when value="files">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	150 <repeat name="rep_factor" title="Factor" min="1">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	151 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	152 <sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	153 <valid initial="string.letters,string.digits"><add value="_" /></valid>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	154 </sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	155 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	156 <repeat name="rep_group" title="Group" min="2" default="2">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	157 <param name="groupName" type="text" label="Name"
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	158 help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	159 <sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	160 <valid initial="string.letters,string.digits"><add value="_" /></valid>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	161 </sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	162 </param>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	163 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	164 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	165 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	166 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	167
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	168 <when value="matrix">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	169 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	170
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	171 <conditional name="fact">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	172 <param name="ffile" type="select" label="Input factor information from file?"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	173 help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	174 <option value="no">No</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	175 <option value="yes">Yes</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	176 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	177 <when value="yes">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	178 <param name="finfo" type="data" format="tabular" label="Factor File"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	179 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	180 <when value="no" >
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	181 <repeat name="rep_factor" title="Factor" min="1">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	182 <param name="factorName" type="text" label="Factor Name"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	183 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	184 <validator type="empty_field" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	185 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	186 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	187 <param name="groupNames" type="text" label="Groups"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	188 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive).">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	189 <validator type="empty_field" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	190 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	191 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	192 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	193 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	194 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	195 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	196 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	197
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	198 <!-- Gene Annotations -->
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	199 <conditional name="anno">
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	200 <param name="annoOpt" type="select" label="Use Gene Annotations?"
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	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.">
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	202 <option value="no">No</option>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	203 <option value="yes">Yes</option>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	204 </param>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	205 <when value="yes">
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	206 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	207 </when>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	208 <when value="no" />
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	209 </conditional>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	210
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	211 <!-- Contrasts -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	212 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	213 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	214 <validator type="empty_field" />
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	215 <validator type="regex" message="Please only use letters, numbers or underscores">^[$\w$-]+$</validator>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	216 </param>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	217 </repeat>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	218
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	219 <!-- Filter Options -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	220 <section name="f" expanded="false" title="Filter Low Counts">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	221 <conditional name="filt">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	222 <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	223 <option value="no" selected="true">No</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	224 <option value="yes">Yes</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	225 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	226 <when value="yes">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	227 <conditional name="cformat">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	228 <param name="format_select" type="select" label="Filter on CPM or Count values?" help="It is slightly better to base the filtering on count-per-million (CPM) rather than the raw count values so as to avoid favoring genes expressed in samples sequenced to a higher depth. ">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	229 <option value="cpm">CPM</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	230 <option value="counts">Counts</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	231 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	232 <when value="cpm">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	233 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	234 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	235 help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	236 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	237 <when value="counts">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	238 <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information." />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	239 <conditional name="samples">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	240 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	241 <option value="total">Total</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	242 <option value="sample">Sample</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	243 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	244 <when value="total">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	245 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	246 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	247 <when value="sample">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	248 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	249 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	250 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	251 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	252 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	253 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	254 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	255 <when value="no" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	256 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	257 </section>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	258
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	259 <!-- Output Options -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	260 <section name="out" expanded="false" title="Output Options">
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	261 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report and as PDFs">
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	262 <option value="d">Density Plots (if filtering)</option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	263 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	264 <option value="b">Box Plots (if normalising)</option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	265 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	266 <option value="m">MD Plots for individual samples</option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	267 <option value="h">Heatmaps (top DE genes) </option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	268 <option value="s">Stripcharts (top DE genes)</option>
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	269 </param>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	270 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	271 label="Output Normalised Counts Table?"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	272 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	273 </param>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	274 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	275 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	276 label="Output RData file?"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	277 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	278 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	279 </section>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	280
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	281 <!-- Advanced Options -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	282 <section name="adv" expanded="false" title="Advanced Options">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	283 <param name="lfc" type="float" value="0" min="0"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	284 label="Minimum Log2 Fold Change"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	285 help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MD plot. Default: 0."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	286 <param name="pVal" type="float" value="0.05" min="0" max="1"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	287 label="P-Value Adjusted Threshold"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	288 help="Genes below this threshold are considered significant and highlighted in the MD plot. If either BH(1995) or BY(2001) are selected then this value is a false-discovery-rate control. If Holm(1979) is selected then this is an adjusted p-value for family-wise error rate. Default: 0.05."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	289 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	290 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	291 <option value="BY">Benjamini and Yekutieli (2001)</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	292 <option value="holm">Holm (1979)</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	293 <option value="none">None</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	294 </param>
6 6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	295 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	296 label="Test significance relative to a fold-change threshold (TREAT)"
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	297 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	298 <param name="topgenes" type="integer" value="10" min="0" max="100"
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	299 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	300 help="The top DE genes will be highlighted in the Volcano plot for each contrast and can be output in heatmap and stripchart PDFs (max 100). Default: 10."/>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	301 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	302 <option value="TMM" selected="true">TMM</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	303 <option value="RLE">RLE</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	304 <option value="upperquartile">Upperquartile</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	305 <option value="none">None (Don't normalise)</option>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	306 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	307 <param name="robOption" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use Robust Settings?" help="Using robust settings is usually recommended to protect against outlier genes. Default: Yes" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	308 </section>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	309
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	310 </inputs>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	311
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	312 <outputs>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	313 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	314 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	315 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	316 </collection>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	317 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	318 <filter>out['rscript']</filter>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	319 </data>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	320 </outputs>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	321
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	322 <tests>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	323 <!-- Ensure report is output -->
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	324 <test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	325 <param name="format" value="matrix" />
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	326 <param name="counts" value="matrix.txt" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	327 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	328 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	329 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	330 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	331 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	332 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	333 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	334 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	335 <param name="contrast" value="WT-Mut" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	336 </repeat>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	337 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	338 <param name="topgenes" value="6" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	339 <output_collection name="outTables" count="2">
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	340 <element name="limma-voom_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	341 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	342 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	343 <has_text_matching expression="11304.*0.4573" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	344 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	345 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	346 <element name="limma-voom_WT-Mut" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	347 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	348 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	349 <has_text_matching expression="11304.*-0.4573" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	350 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	351 </element>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	352 </output_collection>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	353 <output name="outReport" >
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	354 <assert_contents>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	355 <has_text text="Limma Analysis Output" />
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	356 <not_has_text text="RData" />
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	357 </assert_contents>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	358 </output>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	359 </test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	360 <!-- Ensure annotation file input works -->
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	361 <test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	362 <param name="format" value="matrix" />
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	363 <param name="annoOpt" value="yes" />
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	364 <param name="geneanno" value="anno.txt" />
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	365 <param name="counts" value="matrix.txt" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	366 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	367 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	368 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	369 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	370 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	371 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	372 </repeat>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	373 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	374 <param name="topgenes" value="6" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	375 <output_collection name="outTables" count="1">
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	376 <element name="limma-voom_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	377 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	378 <has_text_matching expression="EntrezID.Symbol.logFC.AveExpr.t.P.Value.adj.P.Val.*B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	379 <has_text_matching expression="11304.Abca4.0.4573" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	380 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	381 </element>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	382 </output_collection>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	383 </test>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	384 <!-- Ensure Rscript and RData file can be output -->
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	385 <test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	386 <param name="format" value="matrix" />
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	387 <param name="rscript" value="True"/>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	388 <param name="rdaOption" value="true" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	389 <param name="counts" value="matrix.txt" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	390 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	391 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	392 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	393 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	394 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	395 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	396 </repeat>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	397 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	398 <param name="topgenes" value="6" />
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	399 <output name="outReport" >
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	400 <assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	401 <has_text text="RData" />
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	402 </assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	403 </output>
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	404 <output name="rscript">
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	405 <assert_contents>
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	406 <has_text_matching expression="Task run time" />
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	407 </assert_contents>
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	408 </output>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	409 </test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	410 <!-- Ensure secondary factors work -->
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	411 <test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	412 <param name="format" value="matrix" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	413 <param name="counts" value="matrix.txt" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	414 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	415 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	416 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	417 </repeat>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	418 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	419 <param name="factorName" value="Batch"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	420 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	421 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	422 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	423 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	424 </repeat>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	425 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	426 <param name="topgenes" value="6" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	427 <output_collection name="outTables" count="1" >
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	428 <element name="limma-voom_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	429 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	430 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	431 <has_text_matching expression="11304.*0.4590" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	432 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	433 </element>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	434 </output_collection>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	435 </test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	436 <!-- Ensure factors file input works -->
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	437 <test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	438 <param name="format" value="matrix" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	439 <param name="ffile" value="yes" />
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	440 <param name="finfo" value="factorinfo.txt" />
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	441 <param name="counts" value="matrix.txt" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	442 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	443 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	444 </repeat>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	445 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	446 <param name="topgenes" value="6" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	447 <output_collection name="outTables" count="1">
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	448 <element name="limma-voom_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	449 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	450 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	451 <has_text_matching expression="11304.*0.4590" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	452 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	453 </element>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	454 </output_collection>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	455 </test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	456 <!-- Ensure normalised counts file output works-->
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	457 <test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	458 <param name="format" value="matrix" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	459 <param name="normCounts" value="true" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	460 <param name="counts" value="matrix.txt" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	461 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	462 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	463 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	464 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	465 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	466 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	467 </repeat>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	468 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	469 <param name="topgenes" value="6" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	470 <output_collection name="outTables" count="2">
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	471 <element name="limma-voom_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	472 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	473 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	474 <has_text_matching expression="11304.*0.4573" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	475 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	476 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	477 <element name="limma-voom_normcounts" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	478 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	479 <has_text_matching expression="GeneID.Mut1.Mut2.Mut3.WT1.WT2.WT3" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	480 <has_text_matching expression="11304.*15.7545" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	481 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	482 </element>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	483 </output_collection>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	484 </test>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	485 <!-- Ensure multiple counts files input works -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	486 <test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	487 <param name="format" value="files" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	488 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	489 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	490 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	491 <param name="groupName" value="WT"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	492 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	493 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	494 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	495 <param name="groupName" value="Mut"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	496 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	497 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	498 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	499 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	500 <param name="factorName" value="Batch"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	501 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	502 <param name="groupName" value="b1"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	503 <param name="countsFile" value="WT1.counts,Mut1.counts"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	504 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	505 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	506 <param name="groupName" value="b2"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	507 <param name="countsFile" value="WT2.counts,Mut2.counts"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	508 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	509 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	510 <param name="groupName" value="b3"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	511 <param name="countsFile" value="WT3.counts,Mut3.counts"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	512 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	513 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	514 <param name="annoOpt" value="yes" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	515 <param name="geneanno" value="anno.txt" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	516 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	517 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	518 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	519 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	520 <param name="contrast" value="WT-Mut" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	521 </repeat>
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	522 <param name="topgenes" value="6" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	523 <param name="normCounts" value="true" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	524 <output_collection name="outTables" count="3">
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	525 <element name="limma-voom_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	526 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	527 <has_text_matching expression="logFC.AveExpr.t.P.Value.adj.P.Val.*B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	528 <has_text_matching expression="11304.Abca4.0.4590" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	529 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	530 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	531 <element name="limma-voom_WT-Mut" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	532 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	533 <has_text_matching expression="EntrezID.Symbol.logFC.AveExpr.t.P.Value.adj.P.Val.*B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	534 <has_text_matching expression="11304.Abca4.-0.4590" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	535 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	536 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	537 <element name="limma-voom_normcounts" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	538 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	539 <has_text_matching expression="EntrezID.Symbol.Mut1.Mut2.Mut3.WT1.WT2.*WT3" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	540 <has_text_matching expression="11304.Abca4.15.7545" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	541 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	542 </element>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	543 </output_collection>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	544 </test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	545 <!-- Ensure limma-trend option works -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	546 <test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	547 <param name="format" value="matrix" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	548 <param name="counts" value="matrix.txt" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	549 <repeat name="rep_factor">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	550 <param name="factorName" value="Genotype"/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	551 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	552 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	553 <repeat name="rep_contrast">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	554 <param name="contrast" value="Mut-WT" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	555 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	556 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	557 <param name="topgenes" value="6" />
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	558 <param name="de_select" value="trend" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	559 <param name="rdaOption" value="true" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	560 <output name="outReport" >
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	561 <assert_contents>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	562 <has_text text="The limma-trend method was used" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	563 </assert_contents>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	564 </output>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	565 <output_collection name="outTables" count="1">
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	566 <element name="limma-trend_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	567 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	568 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	569 <has_text_matching expression="11304.*0.4540" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	570 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	571 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	572 </output_collection>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	573 </test>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	574 <!-- Ensure limma-trend option with annotation works -->
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	575 <test>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	576 <param name="format" value="matrix" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	577 <param name="counts" value="matrix.txt" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	578 <param name="annoOpt" value="yes" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	579 <param name="geneanno" value="anno.txt" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	580 <repeat name="rep_factor">
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	581 <param name="factorName" value="Genotype"/>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	582 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	583 </repeat>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	584 <repeat name="rep_contrast">
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	585 <param name="contrast" value="Mut-WT" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	586 </repeat>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	587 <param name="normalisationOption" value="TMM" />
7 5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33 iuc parents: 6 diff changeset	588 <param name="topgenes" value="6" />
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	589 <param name="de_select" value="trend" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	590 <param name="rdaOption" value="true" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	591 <output name="outReport" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	592 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	593 <has_text text="The limma-trend method was used" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	594 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	595 </output>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	596 <output_collection name="outTables" count="1">
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	597 <element name="limma-trend_Mut-WT" ftype="tabular" >
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	598 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	599 <has_text_matching expression="EntrezID.Symbol.logFC.AveExpr.t.P.Value.adj.P.Val.*B" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	600 <has_text_matching expression="11304.*0.4540" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	601 </assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	602 </element>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	603 </output_collection>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	604 </test>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	605 </tests>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	606
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	607 <help><![CDATA[
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	608 .. class:: infomark
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	609
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	610 What it does
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	611
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	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_.
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	613
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	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.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	615
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	616 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	617
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	618 Inputs
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	619
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	620 Differential Expression Method:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	621 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	622 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	623 robust approach to differential expression is to use limma-trend. This approach will usually work well if the
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	624 ratio of the largest library size to the smallest is not more than about 3-fold. When the library sizes are quite variable between samples, then the voom approach is theoretically more powerful than limma-trend. For more information see the excellent `limma User's Guide`_.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	625
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	626 Counts Data:
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	627 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	628
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	629 Example - Separate Count Files:
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	630
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	631 ========== =======
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	632 GeneID WT1
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	633 ---------- -------
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	634 11287 1699
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	635 11298 1905
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	636 11302 6
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	637 11303 2099
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	638 11304 356
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	639 11305 2528
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	640 ========== =======
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	641
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	642 Example - Single Count Matrix:
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	643
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	644 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	645 GeneID WT1 WT2 WT3 Mut1 Mut2 Mut3
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	646 ---------- ------- ------- ------- -------- -------- --------
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	647 11287 1699 1528 1601 1463 1441 1495
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	648 11298 1905 1744 1834 1345 1291 1346
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	649 11302 6 8 7 5 6 5
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	650 11303 2099 1974 2100 1574 1519 1654
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	651 11304 356 312 337 361 397 346
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	652 11305 2528 2438 2493 1762 1942 2027
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	653 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	654
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	655 Gene Annotations:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	656 Optional input for gene annotations, this can contain more
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	657 information about the genes than just an ID number. The annotations will
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	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.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	659
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	660 Example:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	661
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	662 ========== ========== ===================================================
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	663 GeneID Symbol GeneName
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	664 ---------- ---------- ---------------------------------------------------
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	665 11287 Pzp pregnancy zone protein
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	666 11298 Aanat arylalkylamine N-acetyltransferase
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	667 11302 Aatk apoptosis-associated tyrosine kinase
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	668 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	669 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	670 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	671 ========== ========== ===================================================
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	672
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	673 Factor Information:
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	674 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	675
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	676 Example:
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	677
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	678 ========== ============ =========
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	679 Sample Genotype Batch
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	680 ---------- ------------ ---------
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	681 WT1 WT b1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	682 WT2 WT b2
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	683 WT3 WT b3
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	684 Mut1 Mut b1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	685 Mut2 Mut b2
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	686 Mut3 Mut b3
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	687 ========== ============ =========
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	688
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	689 Factor Name: The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	690
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	691 Groups: The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	692
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	693
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	694 Contrasts of Interest:
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	695 The contrasts you wish to make between levels.
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	696 A common contrast would be a simple difference between two levels: "Mut-WT"
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	697 represents the difference between the mutant and wild type genotypes.
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	698 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	699
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	700 Filter Low Counts:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	701 Genes with very low counts across all libraries provide little evidence for differential expression.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	702 In the biological point of view, a gene must be expressed at some minimal level before
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	703 it is likely to be translated into a protein or to be biologically important. In addition, the
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	704 pronounced discreteness of these counts interferes with some of the statistical approximations
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	705 that are used later in the pipeline. These genes should be filtered out prior to further
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	706 analysis.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	707 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	708 for any of the conditions. Users can set their own definition of genes being expressed. Usually
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	709 a gene is required to have a count of 5-10 in a library to be considered expressed in that
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	710 library. Users should also filter with count-per-million (CPM) rather than filtering on the
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	711 counts directly, as the latter does not account for differences in library sizes between samples.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	712
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	713 Option to ignore the genes that do not show significant levels of
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	714 expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	715
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	716 * Minimum CPM: This is the minimum count per million that a gene must have in at
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	717 least the number of samples specified under Minimum Samples.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	718
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	719 * Minimum Count: This is the minimum count that a gene must have. It can be combined with either Filter
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	720 on Total Count or Minimum Samples.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	721
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	722 * Filter on Total Count: This can be used with the Minimum Count filter to keep genes
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	723 with a minimum total read count.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	724
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	725 * Minimum Samples: This is the number of samples in which the Minimum CPM/Count
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	726 requirement must be met in order for that gene to be kept.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	727
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	728 If the Minimum Samples filter is applied, only genes that exhibit a CPM/count greater than the required amount in at least the number of samples specified will be used for analysis. Care should be taken to
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	729 ensure that the sample requirement is appropriate. In the case of an experiment
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	730 with two experimental groups each with two members, if there is a change from
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	731 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	732 then this will cause that gene to fail the criteria. When in doubt simply do not
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	733 filter or consult the `limma User's Guide`_ for filtering recommendations.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	734
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	735 Advanced Options:
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	736
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	737 By default error rate for multiple testing is controlled using Benjamini and
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	738 Hochberg's false discovery rate control at a threshold value of 0.05. However
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	739 there are options to change this to custom values.
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	740
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	741 * Minimum log2-fold-change Required:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	742 In addition to meeting the requirement for the adjusted statistic for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	743 multiple testing, the observation must have an absolute log2-fold-change
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	744 greater than this threshold to be considered significant, thus highlighted
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	745 in the MD plot.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	746
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	747 * Adjusted Threshold:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	748 Set the threshold for the resulting value of the multiple testing control
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	749 method. Only observations whose statistic falls below this value is
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	750 considered significant, thus highlighted in the MD plot.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	751
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	752 * P-Value Adjustment Method:
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	753 Change the multiple testing control method, the options are BH(1995) and
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	754 BY(2001) which are both false discovery rate controls. There is also
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	755 Holm(1979) which is a method for family-wise error rate control.
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	756
6 6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	757 Testing relative to a threshold (TREAT):
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	758 If there are a lot of differentially expressed genes, a fold change threshold can be applied in addition to the P-value threshold to select genes that are more likely to be biologically significant. However, ranking by P-value and discarding genes with small logFCs can increase the false discovery rate. Using the limma TREAT function performs this analysis correctly (`McCarthy and Smyth, 2009`_).
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	759
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	760 Normalisation Method:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	761 The most obvious technical factor that affects the read counts, other than gene expression
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	762 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	763 analysis for varying sequencing depths as represented by differing library sizes. This is
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	764 part of the basic modeling procedure and flows automatically into fold-change or p-value
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	765 calculations. It is always present, and doesn’t require any user intervention.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	766 The second most important technical influence on differential expression is one that is less
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	767 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	768 sample, but does not provide any measure of the total RNA output on a per-cell basis.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	769 This commonly becomes important when a small number of genes are very highly expressed
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	770 in one sample, but not in another. The highly expressed genes can consume a substantial
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	771 proportion of the total library size, causing the remaining genes to be under-sampled in that
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	772 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	773 appear to be down-regulated in that sample . The edgeR `calcNormFactors` function normalizes for RNA composition by finding a set of scaling factors for the library sizes that minimize the log-fold changes between the samples for most genes. The default method for computing these scale factors uses a trimmed mean of M values (TMM) between each pair of samples. We call the product of the original library size and the scaling factor the effective library size. The effective library size replaces the original library size in all downsteam analyses. TMM is the recommended method for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. You can change the normalisation method under Advanced Options above. For more information, see the `calcNormFactors` section in the `edgeR User's Guide`_.
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	774
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	775 Robust Settings
6 6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	776 Option to use robust settings with eBayes or TREAT, used by both limma-voom and limma-trend. Using robust settings is usually recommended to protect against outlier genes, for more information see the `limma User's Guide`_ and `Phipson et al. 2016`_. This is turned on by default.
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	777
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	778 Prior Count:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	779 If the limma-trend method is used, a count (`prior.count`) is added to all counts to avoid taking a log of zero, and damp down the variances of logarithms of low counts. A default of 3 is used, as recommended in the `limma User's Guide`_.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	780
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	781 Apply Sample Weights:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	782 If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	783 used in the statistical analysis but their impact is reduced. Use this
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	784 whenever significant outliers are present. The MDS plotting tool in this package
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	785 is useful for identifying outliers. For more information on this option see Liu et al. (2015).
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	786
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	787
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	788 Outputs
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	789
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	790 This tool outputs
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	791
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	792 * a table of differentially expressed genes for each contrast of interest
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	793 * a HTML report with plots and additional information
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	794 * an interactive Glimma MD plot and table (if annotation file provided)
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	795
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	796 Optionally, under Output Options you can choose to output
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	797
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	798 * a normalised counts table
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	799 * the R script used by this tool
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	800 * an RData file
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	801
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	802 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	803
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	804 Citations:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	805
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	806 Please try to cite the appropriate articles when you publish results obtained using software, as such citation is the main means by which the authors receive credit for their work.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	807
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	808 limma
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	809
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	810 Please cite the paper below for the limma software itself. Please also try
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	811 to cite the appropriate methodology articles that describe the statistical
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	812 methods implemented in limma, depending on which limma functions you are
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	813 using. The methodology articles are listed in Section 2.1 of the `limma
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	814 User's Guide`_.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	815
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	816 * Smyth GK (2005). Limma: linear models for microarray data. In:
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	817 'Bioinformatics and Computational Biology Solutions using R and
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	818 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	819 W. Huber (eds), Springer, New York, pages 397-420.
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	820
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	821 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	822 precision weights unlock linear model analysis tools for
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	823 RNA-seq read counts. Genome Biology 15, R29.
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	824
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	825 * Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	826
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	827 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	828 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	829 for microarray data. BMC Bioinformatics 7, Article 261.
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	830
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	831
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	832 edgeR
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	833
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	834 Please cite the first paper for the software itself and the other papers for
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	835 the various original statistical methods implemented in edgeR. See
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	836 Section 1.2 in the `edgeR User's Guide`_ for more detail.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	837
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	838 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	839 package for differential expression analysis of digital gene expression
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	840 data. Bioinformatics 26, 139-140
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	841
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	842 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	843 differences in tag abundance. Bioinformatics 23, 2881-2887
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	844
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	845 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	846 binomial dispersion, with applications to SAGE data.
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	847 Biostatistics, 9, 321-332
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	848
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	849 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	850 of multifactor RNA-Seq experiments with respect to biological variation.
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	851 Nucleic Acids Research 40, 4288-4297
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	852
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	853 Please report problems or suggestions to: su.s@wehi.edu.au
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	854
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	855 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	856 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	857 .. _here: https://f1000research.com/articles/5-1408/v2
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	858 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	859 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	860 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	861 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
6 6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	862 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553
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1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	864 ]]></help>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	865 <citations>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	866 <citation type="doi">10.1186/gb-2014-15-2-r29</citation>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	867 <citation type="doi">10.1093/nar/gkv412</citation>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	868 </citations>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	869 </tool>

Mercurial > repos > iuc > limma_voom

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