limma_voom: limma_voom.xml annotate

annotate limma_voom.xml @ 25:915cec6d5763 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 55ecaab6d53c6a3f0769f802a4d68a45291f51e9"

author	iuc
date	Tue, 01 Mar 2022 08:03:22 +0000
parents	a871779c3e22
children

rev	line source
24 a871779c3e22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit ac346e409fbf40ffa7ce155dfa0abbf2bfb8adfa" iuc parents: 23 diff changeset	1 <tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy0">
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>
23 f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	5 <macros>
25 915cec6d5763 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 55ecaab6d53c6a3f0769f802a4d68a45291f51e9" iuc parents: 24 diff changeset	6 <token name="@TOOL_VERSION@">3.50.1</token>
23 f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	7 </macros>
21 2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	8 <xrefs>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	9 <xref type="bio.tools">limma</xref>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	10 </xrefs>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	11 <edam_topics>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	12 <edam_topic>topic_3308</edam_topic>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	13 </edam_topics>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	14 <edam_operations>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	15 <edam_operation>operation_3563</edam_operation>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	16 <edam_operation>operation_3223</edam_operation>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	17 </edam_operations>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	18
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	19 <requirements>
23 f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	20 <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement>
24 a871779c3e22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit ac346e409fbf40ffa7ce155dfa0abbf2bfb8adfa" iuc parents: 23 diff changeset	21 <requirement type="package" version="3.36.0">bioconductor-edger</requirement>
21 2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	22 <requirement type="package" version="1.4.36">r-statmod</requirement>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	23 <requirement type="package" version="1.1.1">r-scales</requirement>
25 915cec6d5763 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 55ecaab6d53c6a3f0769f802a4d68a45291f51e9" iuc parents: 24 diff changeset	24 <requirement type="package" version="0.2.21">r-rjson</requirement>
21 2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	25 <requirement type="package" version="1.20.3">r-getopt</requirement>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" iuc parents: 20 diff changeset	26 <requirement type="package" version="3.1.1">r-gplots</requirement>
24 a871779c3e22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit ac346e409fbf40ffa7ce155dfa0abbf2bfb8adfa" iuc parents: 23 diff changeset	27 <requirement type="package" version="2.4.0">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	28 </requirements>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	29
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	30 <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	31 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" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	32 ]]></version_command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	33
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	34 <command detect_errors="exit_code"><![CDATA[
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	35 #import json
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	36 Rscript '$__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	37
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	38 -R '$outReport'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	39 -o '$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	40
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	41 #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	42
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	43 ## 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	44 #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	45 #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	46 #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	47 #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	48 #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	49 #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	50 $count_files.append(str($file))
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	51 #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	52 $temp_factor.append( {str($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	53 #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	54
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	55 $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	56 $temp_factor_names.append([str($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	57 #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	58 -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	59
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	60 #elif $input.format=="matrix":
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	61 -m '$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	62 #if $input.fact.ffile=='yes':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	63 -f '$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	64 #else:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	65 -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	66 #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	67 #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	68
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	69 #if $anno.annoOpt=='yes':
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	70 -a '$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	71 #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	72
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	73 #if $cont.cfile=='yes':
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	74 -C '$cont.cinfo'
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	75 #else:
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	76 -D '${ ','.join( ['%s' % $x.contrast for x in $cont.rep_contrast] ) }'
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	77 #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	78
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	79 #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	80 #if $f.filt.cformat.format_select == 'cpm':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	81 -c '$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	82 -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	83 #elif $f.filt.cformat.format_select == 'counts':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	84 -z '$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	85 #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	86 -y
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	87 #elif $f.filt.cformat.samples.count_select == 'sample':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	88 -s '$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	89 #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	90 #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	91 #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	92
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	93 #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	94 -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	95 #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	96
12 324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	97 #if $out.filtCounts:
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	98 -F
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	99 #end if
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	100
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	101 #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	102 -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	103 #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	104
11 0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	105 #if $out.libinfo:
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	106 -L
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	107 #end if
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	108
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	109 #if $out.rdaOption:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	110 -r
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	111 #end if
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	112
11 0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	113
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	114 -l '$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	115 -p '$adv.pVal'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	116 -d '$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	117 -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	118 #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	119 -T
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	120 #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	121
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	122 #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	123 #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	124 -w
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	125 #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	126 #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	127 -t $deMethod.prior_count
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	128 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	129
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	130 -n '$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	131
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	132 #if $adv.robOption:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	133 -b
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	134 #end if
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	135
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	136 &&
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	137 mkdir ./output_dir
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	138
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	139 &&
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	140 cp '$outReport.files_path'/*tsv output_dir/
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	141
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	142 #if 'i' in str($out.plots).split( "," ):
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	143 && cp -r ./glimma* '$outReport.files_path'
9 a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0 iuc parents: 8 diff changeset	144 #end if
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	145
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	146 #if $out.filtCounts or $out.normCounts:
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	147 && cp '$outReport.files_path'/*counts output_dir/
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	148 #end if
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	149
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	150 #if $out.rscript:
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	151 && cp '$__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	152 #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	153 ]]></command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	154
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	155 <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	156
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	157 <!-- 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	158 <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	159 <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	160 <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	161 <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	162 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	163 <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	164 <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	165 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	166 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	167 </when>
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="trend">
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="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	170 </when>
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>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	172 <!-- 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	173 <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	174 <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	175 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	176 <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	177 <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	178 </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	179
3 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="files">
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">
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	182 <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.">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	183 <sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	184 <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	185 </sanitizer>
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 <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	188 <param name="groupName" type="text" label="Name"
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	189 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	190 <sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	191 <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	192 </sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	193 </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	194 <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	195 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	196 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	197 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	198
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	199 <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	200 <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	201
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	202 <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	203 <param name="ffile" type="select" label="Input factor information from file?"
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	204 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	205 <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	206 <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	207 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	208 <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	209 <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	210 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	211 <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	212 <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	213 <param name="factorName" type="text" label="Factor Name"
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	214 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.">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	215 <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	216 <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	217 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	218 <param name="groupNames" type="text" label="Groups"
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	219 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), the group names MUST not contain hyphens.">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	220 <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	221 <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	222 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	223 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	224 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	225 </conditional>
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>
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>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	228
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	229 <!-- 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	230 <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	231 <param name="annoOpt" type="select" label="Use Gene Annotations?"
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	232 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. Interactive Glimma Volcano and MD plots 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	233 <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	234 <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	235 </param>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	236 <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	237 <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	238 </when>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	239 <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	240 </conditional>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	241
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	242 <!-- Contrasts -->
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	243 <conditional name="cont">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	244 <param name="cfile" type="select" label="Input Contrast information from file?"
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	245 help="You can choose to input the contrast information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens. Use a hyphen to separate the groups you want to compare, as shown in the Help section below.">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	246 <option value="no">No</option>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	247 <option value="yes">Yes</option>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	248 </param>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	249 <when value="yes">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	250 <param name="cinfo" type="data" format="tabular" label="Contrasts File"/>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	251 </when>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	252 <when value="no" >
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	253 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	254 <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-Ctrl1)-(Mut2-Ctrl2). 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">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	255 <validator type="empty_field" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	256 <validator type="regex" message="Please only use letters, numbers or underscores">^[$\w$-]+$</validator>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	257 </param>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	258 </repeat>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	259 </when>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	260 </conditional>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	261
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	262 <!-- 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	263 <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	264 <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	265 <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	266 <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	267 <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	268 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	269 <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	270 <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	271 <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	272 <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	273 <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	274 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	275 <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	276 <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."/>
23 f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	277 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	278 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."/>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	279 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 </param>
23 f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	287 <when value="total"/>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	288 <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	289 <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	290 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	291 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	292 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	293 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	294 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	295 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	296 <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	297 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	298 </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	299
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	300 <!-- 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	301 <section name="out" expanded="false" title="Output Options">
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	302 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report">
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	303 <option value="i" selected="True">Glimma Interactive Plots</option>
8 87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623 iuc parents: 7 diff changeset	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 </param>
12 324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	312 <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	313 label="Output Filtered Counts Table?"
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	314 help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	315 </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	316 <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	317 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	318 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	319 </param>
11 0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	320 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	321 label="Output Library information file?"
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	322 help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No">
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	323 </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	324 <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	325 <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	326 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	327 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	328 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	329 </section>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	330
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	331 <!-- 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	332 <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	333 <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	334 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	335 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	336 <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	337 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	338 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	339 <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	340 <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	341 <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	342 <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	343 <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	344 </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	345 <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	346 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	347 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	348 <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	349 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	350 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	351 <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	352 <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	353 <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	354 <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	355 <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	356 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	357 <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	358 </section>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	359
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	360 </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	361
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	362 <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	363 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	364 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables">
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	365 <discover_datasets pattern="(?P<name>.+)\.tsv$" 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	366 </collection>
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	367 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts">
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	368 <filter>out['filtCounts']</filter>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	369 </data>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	370 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts">
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	371 <filter>out['normCounts']</filter>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	372 </data>
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	373 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	374 <filter>out['rscript']</filter>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	375 </data>
11 0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	376 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	377 <filter>out['libinfo']</filter>
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	378 </data>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	379 </outputs>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	380
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	381 <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	382 <!-- Ensure report is output -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	383 <test expect_num_outputs="2">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	384 <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	385 <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	386 <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	387 <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	388 <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	389 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	390 <param name="cfile" value="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	391 <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	392 <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	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="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	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" />
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	399 <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	400 <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	401 <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	402 <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	403 <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	404 </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	405 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	406 <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	407 <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	408 <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	409 <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	410 </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	411 </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	412 </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	413 <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	414 <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	415 <has_text text="Limma Analysis Output" />
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	416 <has_text text="Glimma Interactive Results" />
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	417 <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	418 </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	419 </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	420 </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	421 <!-- Ensure annotation file input works -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	422 <test expect_num_outputs="2">
3 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="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	424 <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	425 <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	426 <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	427 <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	428 <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	429 <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	430 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	431 <param name="cfile" value="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	432 <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	433 <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	434 </repeat>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	435 <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	436 <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	437 <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	438 <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	439 <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	440 <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	441 <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	442 </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	443 </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	444 </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	445 </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	446 <!-- Ensure Rscript and RData file can be output -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	447 <test expect_num_outputs="3">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	448 <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	449 <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	450 <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	451 <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	452 <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	453 <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	454 <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	455 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	456 <param name="cfile" value="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	457 <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	458 <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	459 </repeat>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	460 <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	461 <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	462 <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	463 <assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	464 <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	465 </assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	466 </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	467 <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	468 <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	469 <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	470 </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	471 </output>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	472 </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	473 <!-- Ensure secondary factors work -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	474 <test expect_num_outputs="2">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	475 <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	476 <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	477 <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	478 <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	479 <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	480 </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	481 <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	482 <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	483 <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	484 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	485 <param name="cfile" value="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	486 <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	487 <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	488 </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	489 <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	490 <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	491 <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	492 <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	493 <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	494 <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	495 <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	496 </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	497 </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	498 </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	499 </test>
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	500 <!-- Ensure factors file with unordered samples works -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	501 <test expect_num_outputs="2">
3 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="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	503 <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	504 <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	505 <param name="counts" value="matrix.txt" />
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	506 <param name="cfile" value="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	507 <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	508 <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	509 </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	510 <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	511 <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	512 <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	513 <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	514 <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	515 <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	516 <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	517 </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	518 </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	519 </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	520 </test>
12 324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	521 <!-- Ensure filtered and normalised count outputs works-->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	522 <test expect_num_outputs="4">
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="format" value="matrix" />
12 324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	524 <param name="filtCounts" 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	525 <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	526 <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	527 <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	528 <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	529 <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	530 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	531 <param name="cfile" value="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	532 <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	533 <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	534 </repeat>
12 324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	535 <param name="filt_select" value="yes" />
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	536 <param name="format_select" value="counts"/>
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	537 <param name="cntReq" value="10"/>
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	538 <param name="count_select" value="sample"/>
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	539 <param name="cntSampleReq" value="3"/>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	540 <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	541 <param name="topgenes" value="6" />
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	542 <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	543 <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	544 <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	545 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
12 324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c iuc parents: 11 diff changeset	546 <has_text_matching expression="11304.0.45.15.52.4.94.7.74.0.0001.5.27" />
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	547 </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	548 </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	549 </output_collection>
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	550 <output name="outNorm" ftype="tabular" >
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	551 <assert_contents>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	552 <has_text_matching expression="GeneID.Mut1.Mut2.Mut3.WT1.WT2.WT3" />
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	553 <has_text_matching expression="11304.15.7.15.8.15.6.15.3.15.2.15.2" />
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	554 </assert_contents>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	555 </output>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	556 <output name="outFilt" ftype="tabular" >
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	557 <assert_contents>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	558 <has_text_matching expression="GeneID.Mut1.Mut2.Mut3.WT1.WT2.WT3" />
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	559 <has_text_matching expression="11304.361.397.346.356.312.337" />
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	560 <not_has_text text="11302"/>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	561 </assert_contents>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	562 </output>
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	563 </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	564 <!-- Ensure multiple counts files input works -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	565 <test expect_num_outputs="3">
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	566 <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	567 <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	568 <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	569 <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	570 <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	571 <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	572 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	573 <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	574 <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	575 <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	576 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	577 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	578 <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	579 <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	580 <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	581 <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	582 <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	583 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	584 <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	585 <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	586 <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	587 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	588 <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	589 <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	590 <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	591 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	592 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	593 <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	594 <param name="geneanno" value="anno.txt" />
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	595 <param name="cfile" value="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	596 <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	597 <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	598 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	599 <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	600 <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	601 </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	602 <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	603 <param name="normCounts" value="true" />
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	604 <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	605 <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	606 <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	607 <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	608 <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	609 </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	610 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	611 <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	612 <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	613 <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	614 <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	615 </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	616 </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	617 </output_collection>
13 a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	618 <output name="outNorm" ftype="tabular" >
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	619 <assert_contents>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	620 <has_text_matching expression="EntrezID.Symbol.Mut1.Mut2.Mut3.WT1.WT2.*WT3" />
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	621 <has_text_matching expression="11304.Abca4.15.7545" />
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	622 </assert_contents>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811 iuc parents: 12 diff changeset	623 </output>
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	624 </test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	625 <!-- Ensure limma-trend option works -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	626 <test expect_num_outputs="2">
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 <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	628 <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	629 <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	630 <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	631 <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	632 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	633 <param name="cfile" value="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	634 <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	635 <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	636 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	637 <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	638 <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	639 <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	640 <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	641 <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	642 <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	643 </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	644 </output>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	645 <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	646 <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	647 <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	648 <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	649 <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	650 </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	651 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	652 </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	653 </test>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	654 <!-- Ensure limma-trend option with annotation works -->
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	655 <test expect_num_outputs="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	656 <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	657 <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	658 <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	659 <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	660 <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	661 <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	662 <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	663 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	664 <param name="cfile" value="no" />
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 <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	666 <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	667 </repeat>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	668 <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	669 <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	670 <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	671 <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	672 <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	673 <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	674 </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	675 </output>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	676 <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	677 <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	678 <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	679 <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	680 <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	681 </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	682 </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	683 </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	684 </test>
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	685 <!-- Ensure samples and groups beginning with numbers can be handled -->
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	686 <test expect_num_outputs="3">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	687 <param name="format" value="matrix" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	688 <param name="counts" value="matrix_num.txt" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	689 <param name="annoOpt" value="yes" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	690 <param name="geneanno" value="anno.txt" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	691 <repeat name="rep_factor">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	692 <param name="factorName" value="Group"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	693 <param name="groupNames" value="2,2,2,1,1,1" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	694 </repeat>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	695 <param name="cfile" value="no" />
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	696 <repeat name="rep_contrast">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	697 <param name="contrast" value="2-1" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	698 </repeat>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	699 <param name="filt_select" value="yes" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	700 <param name="format_select" value="counts"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	701 <param name="cntReq" value="10"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	702 <param name="count_select" value="sample"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	703 <param name="cntSampleReq" value="3"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	704 <param name="normalisationOption" value="TMM" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	705 <param name="normCounts" value="true" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	706 <param name="topgenes" value="6" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	707 <param name="de_select" value="voom" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	708 <output_collection name="outTables" count="1">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	709 <element name="limma-voom_X2-X1" ftype="tabular" >
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	710 <assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	711 <has_text_matching expression="EntrezID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	712 <has_text_matching expression="11304.0.45.15.52.4.94.7.74.0.0001.5.27" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	713 </assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	714 </element>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	715 </output_collection>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	716 <output name="outNorm" ftype="tabular" >
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	717 <assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	718 <has_text_matching expression="EntrezID.2-1.2-2.2-3.1-1.1-2.1-3" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	719 <has_text_matching expression="11304.15.7.15.8.15.6.15.3.15.2.15.2" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	720 </assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	721 </output>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	722 </test>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	723 <!-- Ensure contrasts file works -->
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	724 <test expect_num_outputs="2">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	725 <param name="format" value="matrix" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	726 <param name="counts" value="matrix.txt" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	727 <repeat name="rep_factor">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	728 <param name="factorName" value="Genotype"/>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	729 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	730 </repeat>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	731 <param name="cfile" value="yes" />
23 f5b93d3227ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 22 diff changeset	732 <param name="cinfo" value="contrasts.txt" ftype="tabular" />
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	733 <param name="normalisationOption" value="TMM" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	734 <param name="topgenes" value="6" />
20 455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	735 <output_collection name="outTables" count="3">
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	736 <element name="limma-voom_Mut-WT" ftype="tabular" >
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	737 <assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	738 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	739 <has_text_matching expression="11304.*0.4573" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	740 </assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	741 </element>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	742 <element name="limma-voom_WT-Mut" ftype="tabular" >
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	743 <assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	744 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	745 <has_text_matching expression="11304.*-0.4573" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	746 </assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	747 </element>
20 455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	748 <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	749 <assert_contents>
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	750 <has_text_matching expression="GeneID.logFC.AveExpr.t.P.Value.adj.P.Val.B" />
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	751 <has_text_matching expression="11304.*0.9146" />
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	752 </assert_contents>
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b iuc parents: 19 diff changeset	753 </element>
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	754 </output_collection>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	755 </test>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	756 </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	757
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	758 <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	759 .. class:: infomark
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	760
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	761 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	762
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	763 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. Interactive Glimma_ plots and tables can also be generated and links to the Glimma plots will be provided in the report. 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	764
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	765 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	766
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	767 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	768
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	769 Inputs
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	770
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	771 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	772 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	773 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	774 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	775 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	776
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	777 Counts Data:
16 f564807836a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca iuc parents: 15 diff changeset	778 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. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	779
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	780 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	781
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	782 ========== =======
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	783 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	784 ---------- -------
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	785 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	786 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	787 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	788 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	789 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	790 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	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
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	793 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	794
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	795 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	796 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	797 ---------- ------- ------- ------- -------- -------- --------
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	798 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	799 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	800 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	801 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	802 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	803 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	804 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	805
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	806 Gene Annotations:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	807 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	808 information about the genes than just an ID number. The annotations will
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	809 be available in the differential expression results table and the optional normalised counts table. They will also be used to generate interactive Glimma_ Volcano, MD plots and tables of differential expression. 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	810
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	811 Example:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	812
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	813 ========== ========== ===================================================
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	814 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	815 ---------- ---------- ---------------------------------------------------
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	816 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	817 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	818 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	819 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	820 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	821 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	822 ========== ========== ===================================================
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	823
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	824 Factor Information:
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	825 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count 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	826
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	827 Example:
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	828
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	829 ========== ============ =========
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	830 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	831 ---------- ------------ ---------
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	832 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	833 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	834 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	835 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	836 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	837 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	838 ========== ============ =========
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	839
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	840 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, an additive linear model will be used.
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	841
17 4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597 iuc parents: 16 diff changeset	842 Groups: The names of the groups for the factor. The names should only contain letters, numbers and underscores, other characters such as spaces and hyphens MUST not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. If the group names begin with a number an X will be added as a prefix.
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	843
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	844 Contrasts of Interest:
19 04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	845 The contrasts you wish to make between levels. A common contrast would be a simple difference between two levels: "Mut-WT"
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	846 represents the difference between the mutant and wild type genotypes. Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. Alternatively, a tab-separated file can be input that has the names of the comparisons in the first column and one header row, as shown below.
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	847
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	848 Example:
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	849
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	850 ============= =
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	851 Contrasts
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	852 ------------- -
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	853 Mut-WT
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	854 WT-Mut
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5 iuc parents: 18 diff changeset	855 ============= =
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	856
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	857 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	858 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	859 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	860 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	861 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	862 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	863 analysis.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	864 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	865 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	866 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	867 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	868 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	869
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	870 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	871 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	872
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	873 * 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	874 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	875
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	876 * 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	877 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	878
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	879 * 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	880 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	881
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	882 * 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	883 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	884
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	885 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	886 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	887 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	888 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	889 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	890 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	891
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	892 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	893
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	894 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	895 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	896 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	897
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	898 * 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	899 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	900 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	901 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	902 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	903
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	904 * 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	905 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	906 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	907 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	908
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	909 * 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	910 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	911 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	912 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	913
6 6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	914 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	915 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	916
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	917 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	918 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	919 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	920 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	921 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	922 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	923 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	924 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	925 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	926 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	927 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	928 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	929 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	930 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	931
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	932 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	933 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	934
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	935 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	936 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	937
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	938 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	939 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	940 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	941 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	942 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	943
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	944
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	945 Outputs
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	946
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	947 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	948
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	949 * 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	950 * a HTML report with plots and additional information
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	951
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	952 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	953
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	954 * interactive Glimma plots and tables: MDS plot, and (if annotation file is input) Volcano plot and MD plot (default: Yes)
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	955 * additional plots in the report and as PDFs
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	956 * a normalised counts table
11 0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc iuc parents: 10 diff changeset	957 * a library size information file
4 47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8 iuc parents: 3 diff changeset	958 * 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	959 * 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	960
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	961 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	962
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	963 Citations:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	964
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	965 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	966
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	967 limma
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	968
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	969 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	970 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	971 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	972 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	973 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	974
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	975 * 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	976 '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	977 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	978 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	979
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	980 * 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	981 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	982 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	983
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	984 * 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	985
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	986 * 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	987 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	988 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	989
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	990
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	991 edgeR
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	992
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	993 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	994 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	995 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	996
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	997 * 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	998 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	999 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	1000
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	1001 * 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	1002 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	1003
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	1004 * 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	1005 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	1006 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	1007
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	1008 * 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	1009 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	1010 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	1011
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	1012 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	1013
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	1014 .. _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	1015 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
14 94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5 iuc parents: 13 diff changeset	1016 .. _here: https://f1000research.com/articles/5-1408/v3
3 895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 iuc parents: 2 diff changeset	1017 .. _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	1018 .. _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	1019 .. _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	1020 .. _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	1021 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d iuc parents: 5 diff changeset	1022 .. _Phipson et al. 2016: https://www.ncbi.nlm.nih.gov/pubmed/28367255
1 3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd iuc parents: 0 diff changeset	1023 ]]></help>
0 bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21 iuc parents: diff changeset	1024 <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	1025 <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	1026 <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	1027 </citations>
15 107c169a0b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 31b550aeaf886377ed0feaa7319a7ef3c6b68253 iuc parents: 14 diff changeset	1028 </tool>

Mercurial > repos > iuc > limma_voom

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