Mercurial > repos > iuc > limma_voom

annotate limma_voom.xml @ 13:a984bbe87e2a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
author iuc
date Sun, 30 Sep 2018 10:51:12 -0400
parents 324417ddf9b9
children 94f82c79fa66
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
1 <tool id="limma_voom" name="limma" version="3.34.9.9">
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
2 <description>
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
3 Perform differential expression with limma-voom or limma-trend
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
4 </description>
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
5
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
6 <requirements>
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
7 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
9 <requirement type="package" version="1.4.30">r-statmod</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
10 <requirement type="package" version="0.5.0">r-scales</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
11 <requirement type="package" version="0.2.15">r-rjson</requirement>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
12 <requirement type="package" version="1.20.0">r-getopt</requirement>
7
5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
13 <requirement type="package" version="3.0.1">r-gplots</requirement>
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
14 <requirement type="package" version="1.6.0">bioconductor-glimma</requirement>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
15 </requirements>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
16
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
17 <version_command><![CDATA[
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
18 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
19 ]]></version_command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
20
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
21 <command detect_errors="exit_code"><![CDATA[
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
22 #import json
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
23 Rscript '$__tool_directory__/limma_voom.R'
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
24
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
25 -R '$outReport'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
26 -o '$outReport.files_path'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
27
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
28 #if $input.format=="files":
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
29
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
30 ## Adapted from DESeq2 wrapper
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
31 #set $temp_factor_names = list()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
32 #for $fact in $input.rep_factor:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
33 #set $temp_factor = list()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
34 #for $g in $fact.rep_group:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
35 #set $count_files = list()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
36 #for $file in $g.countsFile:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
37 $count_files.append(str($file))
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
38 #end for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
39 $temp_factor.append( {str($g.groupName): $count_files} )
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
40 #end for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
41
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
42 $temp_factor.reverse()
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
43 $temp_factor_names.append([str($fact.factorName), $temp_factor])
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
44 #end for
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
45 -j '#echo json.dumps(temp_factor_names)#'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
46
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
47 #elif $input.format=="matrix":
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
48 -m '$input.counts'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
49 #if $input.fact.ffile=='yes':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
50 -f '$input.fact.finfo'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
51 #else:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
52 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
53 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
54 #end if
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
55
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
56 #if $anno.annoOpt=='yes':
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
57 -a '$anno.geneanno'
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
58 #end if
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
59
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
60 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
61
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
62 #if $f.filt.filt_select == 'yes':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
63 #if $f.filt.cformat.format_select == 'cpm':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
64 -c '$f.filt.cformat.cpmReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
65 -s '$f.filt.cformat.cpmSampleReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
66 #elif $f.filt.cformat.format_select == 'counts':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
67 -z '$f.filt.cformat.cntReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
68 #if $f.filt.cformat.samples.count_select == 'total':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
69 -y
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
70 #elif $f.filt.cformat.samples.count_select == 'sample':
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
71 -s '$f.filt.cformat.samples.cntSampleReq'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
72 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
73 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
74 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
75
8
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
76 #if $out.plots:
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
77 -P $out.plots
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
78 #end if
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
79
12
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
80 #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
81 -F
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
82 #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
83
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
84 #if $out.normCounts:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
85 -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
86 #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
87
11
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
88 #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
89 -L
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
90 #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
91
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
92 #if $out.rdaOption:
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
93 -r
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
94 #end if
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
95
11
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
96
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
97 -l '$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
98 -p '$adv.pVal'
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
99 -d '$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
100 -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
101 #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
102 -T
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
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
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
105 #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
106 #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
107 -w
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
108 #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
109 #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
110 -t $deMethod.prior_count
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
111 #end if
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
112
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
113 -n '$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
114
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
115 #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
116 -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
117 #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
118
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
119 &&
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
120 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
121
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
122 &&
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
123 #if $anno.annoOpt=='yes':
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
124 cp -r ./glimma* '$outReport.files_path' &&
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
125 #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
126
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
127 cp '$outReport.files_path'/*tsv output_dir/
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
128
13
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
129 #if $out.filtCounts or $out.normCounts:
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
130 && cp '$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
131 #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
132
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
133 #if $out.rscript:
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
134 && cp '$__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
135 #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
136 ]]></command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
137
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
138 <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
139
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
140 <!-- 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
141 <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
142 <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
143 <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
144 <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
145 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
146 <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
147 <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
148 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
149 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
150 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
151 <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
152 <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
153 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
154 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
155 <!-- 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
156 <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
157 <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
158 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
159 <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
160 <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
161 </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
162
3
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="files">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
164 <repeat 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
165 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
166 <sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
167 <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
168 </sanitizer>
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>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
170 <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
171 <param name="groupName" type="text" label="Name"
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
172 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
173 <sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
174 <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
175 </sanitizer>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
176 </param>
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
177 <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
178 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
179 </repeat>
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>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
181
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
182 <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
183 <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
184
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
185 <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
186 <param name="ffile" type="select" label="Input factor information from file?"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
187 help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
188 <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
189 <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
190 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
191 <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
192 <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
193 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
194 <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
195 <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
196 <param name="factorName" type="text" label="Factor Name"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
197 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
198 <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
199 <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
200 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
201 <param name="groupNames" type="text" label="Groups"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
202 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive).">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
203 <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
204 <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
205 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
206 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
207 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
208 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
209 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
210 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
211
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
212 <!-- 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
213 <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
214 <param name="annoOpt" type="select" label="Use Gene Annotations?"
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
215 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene, and used to label the top genes in the Volcano plot. An interactive Glimma MD plot and table will also be generated. See Help section below.">
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
216 <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
217 <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
218 </param>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
219 <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
220 <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
221 </when>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
222 <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
223 </conditional>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
224
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
225 <!-- Contrasts -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
226 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
10
009d442415b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
227 <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">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
228 <validator type="empty_field" />
8
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
229 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
230 </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
231 </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
232
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
233 <!-- 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
234 <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
235 <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
236 <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
237 <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
238 <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
239 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
240 <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
241 <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
242 <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
243 <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
244 <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
245 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
246 <when 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
247 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
248 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
249 help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
250 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
251 <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
252 <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
253 <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
254 <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
255 <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
256 <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
257 </param>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
258 <when value="total">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
259 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
260 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
261 <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
262 <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
263 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
264 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
265 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
266 </when>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
267 </conditional>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
268 </when>
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="no" />
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>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
271 </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
272
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
273 <!-- 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
274 <section name="out" expanded="false" title="Output Options">
8
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
275 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report and as PDFs">
87f26da8078e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
276 <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
277 <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
278 <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
279 <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
280 <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
281 <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
282 <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
283 </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
284 <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
285 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
286 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
287 </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
288 <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
289 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
290 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
291 </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
292 <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
293 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
294 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
295 </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
296 <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
297 <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
298 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
299 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
300 </param>
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>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
302
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
303 <!-- 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
304 <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
305 <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
306 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
307 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
308 <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
309 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
310 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
311 <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
312 <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
313 <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
314 <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
315 <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
316 </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
317 <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
318 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
319 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
320 <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
321 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
322 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
323 <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
324 <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
325 <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
326 <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
327 <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
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 <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
330 </section>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
331
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
332 </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
333
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
334 <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
335 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
13
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
336 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables">
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
337 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" 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
338 </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
339 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts">
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
340 <filter>out['filtCounts']</filter>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
341 </data>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
342 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts">
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
343 <filter>out['normCounts']</filter>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
344 </data>
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
345 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
346 <filter>out['rscript']</filter>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
347 </data>
11
0433416377de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
348 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${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
349 <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
350 </data>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
351 </outputs>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
352
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
353 <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
354 <!-- Ensure report is output -->
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
355 <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
356 <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
357 <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
358 <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
359 <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
360 <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
361 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
362 <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
363 <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
364 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
365 <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
366 <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
367 </repeat>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
368 <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
369 <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
370 <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
371 <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
372 <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
373 <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
374 <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
375 </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
376 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
377 <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
378 <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
379 <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
380 <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
381 </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
382 </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
383 </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
384 <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
385 <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
386 <has_text text="Limma Analysis Output" />
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
387 <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
388 </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
389 </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
390 </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
391 <!-- Ensure annotation file input works -->
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
392 <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
393 <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
394 <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
395 <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
396 <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
397 <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
398 <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
399 <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
400 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
401 <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
402 <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
403 </repeat>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
404 <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
405 <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
406 <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
407 <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
408 <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
409 <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
410 <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
411 </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
412 </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
413 </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
414 </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
415 <!-- Ensure Rscript and RData file can be output -->
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
416 <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
417 <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
418 <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
419 <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
420 <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
421 <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
422 <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
423 <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
424 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
425 <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
426 <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
427 </repeat>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
428 <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
429 <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
430 <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
431 <assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
432 <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
433 </assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
434 </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
435 <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
436 <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
437 <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
438 </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
439 </output>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
440 </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
441 <!-- Ensure secondary factors work -->
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
442 <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
443 <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
444 <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
445 <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
446 <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
447 <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
448 </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
449 <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
450 <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
451 <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
452 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
453 <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
454 <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
455 </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
456 <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
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 </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
464 </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
465 </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
466 </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
467 <!-- Ensure factors file input works -->
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
468 <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
469 <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
470 <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
471 <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
472 <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
473 <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
474 <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
475 </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
476 <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
477 <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
478 <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
479 <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
480 <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
481 <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
482 <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
483 </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
484 </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
485 </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
486 </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
487 <!-- Ensure filtered and normalised count outputs works-->
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
488 <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
489 <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
490 <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
491 <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
492 <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
493 <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
494 <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
495 <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
496 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
497 <repeat 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
498 <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
499 </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
500 <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
501 <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
502 <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
503 <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
504 <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
505 <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
506 <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
507 <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
508 <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
509 <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
510 <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
511 <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
512 </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
513 </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
514 </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
515 <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
516 <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
517 <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
518 <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
519 </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
520 </output>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
521 <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
522 <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
523 <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
524 <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
525 <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
526 </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
527 </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
528 </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
529 <!-- Ensure multiple counts files input works -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
530 <test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
531 <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
532 <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
533 <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
534 <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
535 <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
536 <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
537 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
538 <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
539 <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
540 <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
541 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
542 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
543 <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
544 <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
545 <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
546 <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
547 <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
548 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
549 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
550 <param name="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
551 <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
552 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
553 <repeat name="rep_group">
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
554 <param name="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
555 <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
556 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
557 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
558 <param name="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
559 <param name="geneanno" value="anno.txt" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
560 <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
561 <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
562 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
563 <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
564 <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
565 </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
566 <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
567 <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
568 <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
569 <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
570 <assert_contents>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
571 <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
572 <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
573 </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
574 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
575 <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
576 <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
577 <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
578 <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
579 </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
580 </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
581 </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
582 <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
583 <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
584 <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
585 <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
586 </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
587 </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
588 </test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
589 <!-- Ensure limma-trend option works -->
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
590 <test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
591 <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
592 <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
593 <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
594 <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
595 <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
596 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
597 <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
598 <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
599 </repeat>
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="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
601 <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
602 <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
603 <param name="rdaOption" value="true" />
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
604 <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
605 <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
606 <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
607 </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
608 </output>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
609 <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
610 <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
611 <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
612 <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
613 <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
614 </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
615 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
616 </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
617 </test>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
618 <!-- Ensure limma-trend option with annotation works -->
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
619 <test>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
620 <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
621 <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
622 <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
623 <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
624 <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
625 <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
626 <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
627 </repeat>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
628 <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
629 <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
630 </repeat>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
631 <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
632 <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
633 <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
634 <param name="rdaOption" value="true" />
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
635 <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
636 <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
637 <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
638 </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
639 </output>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
640 <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
641 <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
642 <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
643 <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
644 <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
645 </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
646 </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
647 </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
648 </test>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
649 </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
650
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
651 <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
652 .. class:: infomark
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
653
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
654 **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
655
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
656 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. If an annotation file is provided, interactive Glimma_ plots and a table of differentially expressed genes will also be generated. See an example workflow here_.
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
657
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
658 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
659
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
660 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
661
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
662 **Inputs**
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
663
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
664 **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
665 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
666 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
667 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
668 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
669
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
670 **Counts Data:**
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
671 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
672
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
673 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
674
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
675 ========== =======
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
676 **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
677 ---------- -------
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
678 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
679 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
680 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
681 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
682 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
683 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
684 ========== =======
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
685
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
686 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
687
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
688 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
689 **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
690 ---------- ------- ------- ------- -------- -------- --------
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
691 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
692 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
693 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
694 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
695 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
696 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
697 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
698
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
699 **Gene Annotations:**
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
700 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
701 information about the genes than just an ID number. The annotations will
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
702 be available in the differential expression results table and the optional normalised counts table. They will also be used to generate interactive Glimma_ MD plots and table of differential expression, a link to the Glimma plots will be provided in the report. The input annotation file must contain a header row and have the gene IDs in the first column. The second column will be used to label the genes in the Volcano plot and interactive Glimma plots, additional columns will be available in the Glimma interactive table. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
703
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
704 Example:
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
705
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
706 ========== ========== ===================================================
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
707 **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
708 ---------- ---------- ---------------------------------------------------
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
709 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
710 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
711 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
712 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
713 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
714 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
715 ========== ========== ===================================================
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
716
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
717 **Factor Information:**
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
718 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
719
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
720 Example:
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
721
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
722 ========== ============ =========
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
723 **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
724 ---------- ------------ ---------
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
725 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
726 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
727 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
728 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
729 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
730 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
731 ========== ============ =========
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
732
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
733 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
734
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
735 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
736
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
737
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
738 **Contrasts of Interest:**
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
739 The contrasts you wish to make between levels.
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
740 A common contrast would be a simple difference between two levels: "Mut-WT"
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
741 represents the difference between the mutant and wild type genotypes.
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
742 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
743
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
744 **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
745 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
746 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
747 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
748 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
749 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
750 analysis.
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
751 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
752 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
753 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
754 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
755 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
756
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
757 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
758 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
759
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
760 * **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
761 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
762
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
763 * **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
764 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
765
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
766 * **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
767 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
768
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
769 * **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
770 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
771
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
772 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
773 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
774 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
775 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
776 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
777 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
778
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 **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
780
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
781 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
782 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
783 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
784
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
785 * **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
786 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
787 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
788 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
789 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
790
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
791 * **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
792 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
793 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
794 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
795
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
796 * **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
797 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
798 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
799 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
800
6
6c9be744c932 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
801 **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
802 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
803
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
804 **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
805 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
806 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
807 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
808 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
809 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
810 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
811 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
812 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
813 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
814 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
815 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
816 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
817 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
818
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
819 **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
820 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
821
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
822 **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
823 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
824
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
825 **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
826 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
827 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
828 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
829 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
830
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
831
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
832 **Outputs**
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
833
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
834 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
835
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
836 * 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
837 * a HTML report with plots and additional information
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
838 * an interactive Glimma MD plot and table (if annotation file provided)
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
839
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
840 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
841
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
842 * 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
843 * 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
844 * 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
845 * 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
846
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
847 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
848
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
849 **Citations:**
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
850
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
851 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
852
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
853 limma
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
854
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
855 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
856 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
857 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
858 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
859 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
860
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
861 * 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
862 '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
863 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
864 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
865
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
866 * 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
867 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
868 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
869
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
870 * 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
871
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
872 * 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
873 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
874 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
875
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
876
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
877 edgeR
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
878
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
879 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
880 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
881 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
882
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
883 * 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
884 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
885 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
886
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
887 * 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
888 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
889
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
890 * 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
891 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
892 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
893
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
894 * 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
895 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
896 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
897
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
898 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
899
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
900 .. _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
901 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
902 .. _here: https://f1000research.com/articles/5-1408/v2
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
903 .. _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
904 .. _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
905 .. _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
906 .. _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
907 .. _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
908 .. _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
909 ]]></help>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
910 <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
911 <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
912 <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
913 </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
914 </tool>