Mercurial > repos > iuc > limma_voom

annotate limma_voom.xml @ 21:2a2ab192ccac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
author iuc
date Fri, 04 Jun 2021 20:36:33 +0000
parents 455d6445a6a0
children 8fc8a0e462bf
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2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
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1 <tool id="limma_voom" name="limma" version="3.48.0">
0
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2 <description>
3
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3 Perform differential expression with limma-voom or limma-trend
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4 </description>
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2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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5 <xrefs>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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6 <xref type="bio.tools">limma</xref>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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7 </xrefs>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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8 <edam_topics>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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9 <edam_topic>topic_3308</edam_topic>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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10 </edam_topics>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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11 <edam_operations>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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12 <edam_operation>operation_3563</edam_operation>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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13 <edam_operation>operation_3223</edam_operation>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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14 </edam_operations>
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15
0
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16 <requirements>
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17 <requirement type="package" version="3.48.0">bioconductor-limma</requirement>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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18 <requirement type="package" version="3.34.0">bioconductor-edger</requirement>
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19 <requirement type="package" version="1.4.36">r-statmod</requirement>
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20 <requirement type="package" version="1.1.1">r-scales</requirement>
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21 <requirement type="package" version="0.2.20">r-rjson</requirement>
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22 <requirement type="package" version="1.20.3">r-getopt</requirement>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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23 <requirement type="package" version="3.1.1">r-gplots</requirement>
2a2ab192ccac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
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24 <requirement type="package" version="2.2.0">bioconductor-glimma</requirement>
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25 </requirements>
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26
1
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27 <version_command><![CDATA[
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28 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" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
1
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29 ]]></version_command>
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3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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31 <command detect_errors="exit_code"><![CDATA[
3
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32 #import json
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33 Rscript '$__tool_directory__/limma_voom.R'
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34
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35 -R '$outReport'
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36 -o '$outReport.files_path'
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37
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38 #if $input.format=="files":
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39
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40 ## Adapted from DESeq2 wrapper
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41 #set $temp_factor_names = list()
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42 #for $fact in $input.rep_factor:
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43 #set $temp_factor = list()
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44 #for $g in $fact.rep_group:
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45 #set $count_files = list()
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46 #for $file in $g.countsFile:
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47 $count_files.append(str($file))
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48 #end for
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49 $temp_factor.append( {str($g.groupName): $count_files} )
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50 #end for
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51
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52 $temp_factor.reverse()
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53 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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54 #end for
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55 -j '#echo json.dumps(temp_factor_names)#'
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56
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57 #elif $input.format=="matrix":
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58 -m '$input.counts'
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59 #if $input.fact.ffile=='yes':
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60 -f '$input.fact.finfo'
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61 #else:
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62 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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63 #end if
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64 #end if
1
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66 #if $anno.annoOpt=='yes':
3
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67 -a '$anno.geneanno'
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68 #end if
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69
19
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70 #if $cont.cfile=='yes':
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71 -C '$cont.cinfo'
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72 #else:
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73 -D '${ ','.join( ['%s' % $x.contrast for x in $cont.rep_contrast] ) }'
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74 #end if
1
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75
3
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76 #if $f.filt.filt_select == 'yes':
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77 #if $f.filt.cformat.format_select == 'cpm':
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78 -c '$f.filt.cformat.cpmReq'
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79 -s '$f.filt.cformat.cpmSampleReq'
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80 #elif $f.filt.cformat.format_select == 'counts':
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81 -z '$f.filt.cformat.cntReq'
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82 #if $f.filt.cformat.samples.count_select == 'total':
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diff changeset
83 -y
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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84 #elif $f.filt.cformat.samples.count_select == 'sample':
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85 -s '$f.filt.cformat.samples.cntSampleReq'
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86 #end if
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87 #end if
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88 #end if
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89
8
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90 #if $out.plots:
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91 -P $out.plots
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92 #end if
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93
12
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
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94 #if $out.filtCounts:
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95 -F
324417ddf9b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
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96 #end if
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97
3
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98 #if $out.normCounts:
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99 -x
1
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100 #end if
0
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101
11
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102 #if $out.libinfo:
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103 -L
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104 #end if
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105
3
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106 #if $out.rdaOption:
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107 -r
1
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108 #end if
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109
11
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110
3
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111 -l '$adv.lfc'
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112 -p '$adv.pVal'
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113 -d '$adv.pAdjust'
7
5a722ae502b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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114 -G '$adv.topgenes'
6
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115 #if $adv.treat:
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116 -T
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117 #end if
0
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118
3
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119 #if $deMethod.de_select == 'voom':
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120 #if $deMethod.weightOption:
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121 -w
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122 #end if
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123 #elif $deMethod.de_select == 'trend':
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124 -t $deMethod.prior_count
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125 #end if
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126
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127 -n '$adv.normalisationOption'
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128
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129 #if $adv.robOption:
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130 -b
1
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131 #end if
0
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132
1
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133 &&
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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134 mkdir ./output_dir
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135
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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136 &&
14
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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137 cp '$outReport.files_path'/*tsv output_dir/
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138
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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139 #if 'i' in str($out.plots).split( "," ):
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140 && cp -r ./glimma* '$outReport.files_path'
9
a30e66a28451 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
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141 #end if
13
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142
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143 #if $out.filtCounts or $out.normCounts:
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144 && cp '$outReport.files_path'/*counts output_dir/
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145 #end if
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146
4
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147 #if $out.rscript:
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148 && cp '$__tool_directory__/limma_voom.R' '$rscript'
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149 #end if
1
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150 ]]></command>
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151
0
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152 <inputs>
3
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153
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154 <!-- DE Method Option -->
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155 <conditional name="deMethod">
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156 <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">
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157 <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
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158 <option value="trend">limma-trend</option>
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159 </param>
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160 <when value="voom">
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iuc
parents: 2
diff changeset
161 <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
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162 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False.">
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diff changeset
163 </param>
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diff changeset
164 </when>
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165 <when value="trend">
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166 <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." />
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167 </when>
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diff changeset
168 </conditional>
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diff changeset
169 <!-- Counts and Factors -->
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diff changeset
170 <conditional name="input">
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171 <param name="format" type="select" label="Count Files or Matrix?"
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iuc
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172 help="You can choose to input either separate count files (one per sample) or a single count matrix">
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173 <option value="files">Separate Count Files</option>
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174 <option value="matrix">Single Count Matrix</option>
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175 </param>
1
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176
3
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177 <when value="files">
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178 <repeat name="rep_factor" title="Factor" min="1">
17
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179 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
3
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180 <sanitizer>
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181 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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182 </sanitizer>
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183 </param>
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184 <repeat name="rep_group" title="Group" min="2" default="2">
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185 <param name="groupName" type="text" label="Name"
17
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186 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
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187 <sanitizer>
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188 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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189 </sanitizer>
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190 </param>
4
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191 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
3
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192 </repeat>
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193 </repeat>
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194 </when>
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195
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196 <when value="matrix">
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197 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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198
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199 <conditional name="fact">
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200 <param name="ffile" type="select" label="Input factor information from file?"
17
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201 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
3
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202 <option value="no">No</option>
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203 <option value="yes">Yes</option>
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204 </param>
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205 <when value="yes">
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206 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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207 </when>
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208 <when value="no" >
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209 <repeat name="rep_factor" title="Factor" min="1">
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210 <param name="factorName" type="text" label="Factor Name"
17
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211 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
3
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212 <validator type="empty_field" />
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213 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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214 </param>
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215 <param name="groupNames" type="text" label="Groups"
17
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216 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
3
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217 <validator type="empty_field" />
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218 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
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219 </param>
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220 </repeat>
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221 </when>
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222 </conditional>
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223 </when>
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224 </conditional>
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225
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226 <!-- Gene Annotations -->
0
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227 <conditional name="anno">
1
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228 <param name="annoOpt" type="select" label="Use Gene Annotations?"
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229 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene, and used to label the top genes in the Volcano plot. Interactive Glimma Volcano and MD plots will also be generated. See Help section below.">
0
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230 <option value="no">No</option>
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231 <option value="yes">Yes</option>
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232 </param>
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233 <when value="yes">
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234 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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235 </when>
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236 <when value="no" />
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237 </conditional>
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238
3
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239 <!-- Contrasts -->
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240 <conditional name="cont">
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241 <param name="cfile" type="select" label="Input Contrast information from file?"
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242 help="You can choose to input the contrast information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens. Use a hyphen to separate the groups you want to compare, as shown in the Help section below.">
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243 <option value="no">No</option>
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244 <option value="yes">Yes</option>
0
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245 </param>
19
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246 <when value="yes">
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247 <param name="cinfo" type="data" format="tabular" label="Contrasts File"/>
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248 </when>
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249 <when value="no" >
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250 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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251 <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">
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252 <validator type="empty_field" />
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253 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
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254 </param>
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255 </repeat>
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256 </when>
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257 </conditional>
1
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258
3
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259 <!-- Filter Options -->
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260 <section name="f" expanded="false" title="Filter Low Counts">
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261 <conditional name="filt">
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262 <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">
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263 <option value="no" selected="true">No</option>
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264 <option value="yes">Yes</option>
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265 </param>
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266 <when value="yes">
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267 <conditional name="cformat">
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268 <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. ">
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269 <option value="cpm">CPM</option>
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270 <option value="counts">Counts</option>
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271 </param>
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272 <when value="cpm">
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273 <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."/>
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274 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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275 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."/>
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276 </when>
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277 <when value="counts">
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278 <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." />
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279 <conditional name="samples">
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280 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
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281 <option value="total">Total</option>
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282 <option value="sample">Sample</option>
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283 </param>
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284 <when value="total">
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285 <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." />
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286 </when>
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287 <when value="sample">
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288 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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289 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."/>
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290 </when>
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291 </conditional>
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292 </when>
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293 </conditional>
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294 </when>
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295 <when value="no" />
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296 </conditional>
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297 </section>
1
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298
3
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299 <!-- Output Options -->
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300 <section name="out" expanded="false" title="Output Options">
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301 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report">
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302 <option value="i" selected="True">Glimma Interactive Plots</option>
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303 <option value="d">Density Plots (if filtering)</option>
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304 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
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305 <option value="b">Box Plots (if normalising)</option>
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306 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
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307 <option value="m">MD Plots for individual samples</option>
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308 <option value="h">Heatmaps (top DE genes) </option>
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309 <option value="s">Stripcharts (top DE genes)</option>
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310 </param>
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311 <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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312 label="Output Filtered Counts Table?"
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313 help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
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314 </param>
3
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315 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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316 label="Output Normalised Counts Table?"
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317 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
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318 </param>
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319 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
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320 label="Output Library information file?"
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321 help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No">
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322 </param>
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323 <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
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324 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
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325 label="Output RData file?"
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326 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">
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327 </param>
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328 </section>
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329
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330 <!-- Advanced Options -->
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331 <section name="adv" expanded="false" title="Advanced Options">
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332 <param name="lfc" type="float" value="0" min="0"
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333 label="Minimum Log2 Fold Change"
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334 help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MD plot. Default: 0."/>
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335 <param name="pVal" type="float" value="0.05" min="0" max="1"
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336 label="P-Value Adjusted Threshold"
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337 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."/>
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338 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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339 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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340 <option value="BY">Benjamini and Yekutieli (2001)</option>
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341 <option value="holm">Holm (1979)</option>
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342 <option value="none">None</option>
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343 </param>
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344 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
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345 label="Test significance relative to a fold-change threshold (TREAT)"
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346 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"/>
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347 <param name="topgenes" type="integer" value="10" min="0" max="100"
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348 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
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349 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
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350 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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351 <option value="TMM" selected="true">TMM</option>
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352 <option value="RLE">RLE</option>
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353 <option value="upperquartile">Upperquartile</option>
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354 <option value="none">None (Don't normalise)</option>
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355 </param>
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356 <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" />
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357 </section>
0
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358
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359 </inputs>
1
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360
0
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361 <outputs>
1
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362 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
13
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363 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables">
0
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364 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
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365 </collection>
13
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366 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts">
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367 <filter>out['filtCounts']</filter>
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368 </data>
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369 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts">
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370 <filter>out['normCounts']</filter>
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371 </data>
4
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372 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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373 <filter>out['rscript']</filter>
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374 </data>
11
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375 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
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376 <filter>out['libinfo']</filter>
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377 </data>
0
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378 </outputs>
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379
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380 <tests>
3
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381 <!-- Ensure report is output -->
17
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382 <test expect_num_outputs="2">
3
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383 <param name="format" value="matrix" />
0
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384 <param name="counts" value="matrix.txt" />
3
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385 <repeat name="rep_factor">
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386 <param name="factorName" value="Genotype"/>
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387 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
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388 </repeat>
19
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389 <param name="cfile" value="no" />
3
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390 <repeat name="rep_contrast">
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391 <param name="contrast" value="Mut-WT" />
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392 </repeat>
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393 <repeat name="rep_contrast">
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394 <param name="contrast" value="WT-Mut" />
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395 </repeat>
0
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396 <param name="normalisationOption" value="TMM" />
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397 <param name="topgenes" value="6" />
1
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398 <output_collection name="outTables" count="2">
4
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399 <element name="limma-voom_Mut-WT" ftype="tabular" >
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400 <assert_contents>
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401 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
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402 <has_text_matching expression="11304.*0.4573" />
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403 </assert_contents>
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404 </element>
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405 <element name="limma-voom_WT-Mut" ftype="tabular" >
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406 <assert_contents>
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407 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
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408 <has_text_matching expression="11304.*-0.4573" />
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409 </assert_contents>
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410 </element>
1
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411 </output_collection>
0
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412 <output name="outReport" >
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413 <assert_contents>
3
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414 <has_text text="Limma Analysis Output" />
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415 <has_text text="Glimma Interactive Results" />
0
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416 <not_has_text text="RData" />
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417 </assert_contents>
1
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418 </output>
4
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419 </test>
3
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420 <!-- Ensure annotation file input works -->
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diff changeset
421 <test expect_num_outputs="2">
3
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422 <param name="format" value="matrix" />
0
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diff changeset
423 <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
424 <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:
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425 <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
426 <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
427 <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
428 <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
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429 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
430 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
431 <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
432 <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
433 </repeat>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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434 <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
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435 <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
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436 <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
437 <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
438 <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
439 <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
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440 <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
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441 </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
442 </element>
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
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443 </output_collection>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
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444 </test>
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
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445 <!-- Ensure Rscript and RData file can be output -->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
446 <test expect_num_outputs="3">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
447 <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
448 <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
449 <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
450 <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
451 <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
452 <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
453 <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
454 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
455 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
456 <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
457 <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
458 </repeat>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
459 <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
460 <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
461 <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
462 <assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
463 <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
464 </assert_contents>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
465 </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
466 <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
467 <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
468 <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
469 </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
470 </output>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
471 </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
472 <!-- Ensure secondary factors work -->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
473 <test expect_num_outputs="2">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
474 <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
475 <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
476 <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
477 <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
478 <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
479 </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
480 <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
481 <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
482 <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
483 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
484 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
485 <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
486 <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
487 </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
488 <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
489 <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
490 <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
491 <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
492 <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
493 <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
494 <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
495 </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
496 </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
497 </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
498 </test>
14
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents: 13
diff changeset
499 <!-- Ensure factors file with unordered samples works -->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
500 <test expect_num_outputs="2">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
501 <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
502 <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
503 <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
504 <param name="counts" value="matrix.txt" />
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
505 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
506 <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
507 <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
508 </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
509 <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
510 <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
511 <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
512 <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
513 <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
514 <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
515 <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
516 </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
517 </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
518 </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
519 </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
520 <!-- Ensure filtered and normalised count outputs works-->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
521 <test expect_num_outputs="4">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
522 <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
523 <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
524 <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
525 <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
526 <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
527 <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
528 <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
529 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
530 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
531 <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
532 <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
533 </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
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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
541 <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
542 <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
543 <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
544 <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
545 <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
546 </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
547 </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
548 </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
549 <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
550 <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
551 <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
552 <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
553 </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
554 </output>
a984bbe87e2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
555 <output 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
556 <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
557 <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
558 <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
559 <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
560 </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
561 </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
562 </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
563 <!-- Ensure multiple counts files input works -->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
564 <test expect_num_outputs="3">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
565 <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
566 <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
567 <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
568 <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
569 <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
570 <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
571 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
572 <repeat 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
573 <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
574 <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
575 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
576 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
577 <repeat 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
578 <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
579 <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
580 <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
581 <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
582 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
583 <repeat 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
584 <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
585 <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
586 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
587 <repeat 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
588 <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
589 <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
590 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
591 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
592 <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
593 <param name="geneanno" value="anno.txt" />
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
594 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
595 <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
596 <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
597 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
598 <repeat 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
599 <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
600 </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
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="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
603 <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
604 <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
605 <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
606 <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
607 <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
608 </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
609 </element>
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-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
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="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
613 <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
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>
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
616 </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
617 <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
618 <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
619 <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
620 <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
621 </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
622 </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
623 </test>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
624 <!-- Ensure limma-trend option works -->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
625 <test expect_num_outputs="2">
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
626 <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
627 <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
628 <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
629 <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
630 <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
631 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
632 <param name="cfile" value="no" />
3
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
633 <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
634 <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
635 </repeat>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
636 <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
637 <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
638 <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
639 <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
640 <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
641 <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
642 </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
643 </output>
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
644 <output_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
645 <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
646 <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
647 <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
648 <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
649 </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
650 </element>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
651 </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
652 </test>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
653 <!-- Ensure limma-trend option with annotation works -->
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
654 <test expect_num_outputs="2">
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
655 <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
656 <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
657 <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
658 <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
659 <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
660 <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
661 <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
662 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
663 <param name="cfile" value="no" />
4
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
664 <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
665 <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
666 </repeat>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
667 <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
668 <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
669 <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
670 <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
671 <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
672 <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
673 </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
674 </output>
47cf8073da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
675 <output_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
676 <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
677 <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
678 <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
679 <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
680 </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
681 </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
682 </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
683 </test>
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
684 <!-- Ensure samples and groups beginning with numbers can be handled -->
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
685 <test expect_num_outputs="3">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
686 <param name="format" value="matrix" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
687 <param name="counts" value="matrix_num.txt" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
688 <param name="annoOpt" value="yes" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
689 <param name="geneanno" value="anno.txt" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
690 <repeat name="rep_factor">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
691 <param name="factorName" value="Group"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
692 <param name="groupNames" value="2,2,2,1,1,1" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
693 </repeat>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
694 <param name="cfile" value="no" />
17
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
695 <repeat name="rep_contrast">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
696 <param name="contrast" value="2-1" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
697 </repeat>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
698 <param name="filt_select" value="yes" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
699 <param name="format_select" value="counts"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
700 <param name="cntReq" value="10"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
701 <param name="count_select" value="sample"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
702 <param name="cntSampleReq" value="3"/>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
703 <param name="normalisationOption" value="TMM" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
704 <param name="normCounts" value="true" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
705 <param name="topgenes" value="6" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
706 <param name="de_select" value="voom" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
707 <output_collection name="outTables" count="1">
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
708 <element name="limma-voom_X2-X1" ftype="tabular" >
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
709 <assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
710 <has_text_matching expression="EntrezID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
711 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
712 </assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
713 </element>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
714 </output_collection>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
715 <output name="outNorm" ftype="tabular" >
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
716 <assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
717 <has_text_matching expression="EntrezID.*2-1.*2-2.*2-3.*1-1.*1-2.*1-3" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
718 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
719 </assert_contents>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
720 </output>
4bd4353bfe5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
721 </test>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
722 <!-- Ensure contrasts file works -->
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
723 <test expect_num_outputs="2">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
724 <param name="format" value="matrix" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
725 <param name="counts" value="matrix.txt" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
726 <repeat name="rep_factor">
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
727 <param name="factorName" value="Genotype"/>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
728 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
729 </repeat>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
730 <param name="cfile" value="yes" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
731 <param name="cinfo" value="contrasts.txt" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
732 <param name="normalisationOption" value="TMM" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
733 <param name="topgenes" value="6" />
20
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
734 <output_collection name="outTables" count="3">
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
735 <element name="limma-voom_Mut-WT" ftype="tabular" >
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
736 <assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
737 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
738 <has_text_matching expression="11304.*0.4573" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
739 </assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
740 </element>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
741 <element name="limma-voom_WT-Mut" ftype="tabular" >
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
742 <assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
743 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
744 <has_text_matching expression="11304.*-0.4573" />
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
745 </assert_contents>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
746 </element>
20
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
747 <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
748 <assert_contents>
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
749 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
750 <has_text_matching expression="11304.*0.9146" />
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
751 </assert_contents>
455d6445a6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents: 19
diff changeset
752 </element>
19
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
753 </output_collection>
04cb660cbf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
754 </test>
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
755 </tests>
1
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iuc
parents: 0
diff changeset
756
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
757 <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
758 .. class:: infomark
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
759
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
760 **What it does**
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
761
14
94f82c79fa66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents: 13
diff changeset
762 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. Interactive Glimma_ plots and tables can also be generated and links to the Glimma plots will be provided in the report. See an example workflow here_.
3
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iuc
parents: 2
diff changeset
763
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
764 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
765
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
766 -----
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
767
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768 **Inputs**
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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769
3
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770 **Differential Expression Method:**
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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771 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom.
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772 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
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773 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
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774 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`_.
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775
0
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776 **Counts Data:**
16
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777 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
3
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parents: 2
diff changeset
778
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779 Example - **Separate Count Files**:
0
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780
3
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parents: 2
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781 ========== =======
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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782 **GeneID** **WT1**
895d310ddb21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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783 ---------- -------
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784 11287 1699
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785 11298 1905
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786 11302 6
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787 11303 2099
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788 11304 356
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789 11305 2528
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790 ========== =======
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791
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792 Example - **Single Count Matrix**:
0
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diff changeset
793
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794 ========== ======= ======= ======= ======== ======== ========
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795 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
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796 ---------- ------- ------- ------- -------- -------- --------
1
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797 11287 1699 1528 1601 1463 1441 1495
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798 11298 1905 1744 1834 1345 1291 1346
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799 11302 6 8 7 5 6 5
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800 11303 2099 1974 2100 1574 1519 1654
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801 11304 356 312 337 361 397 346
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802 11305 2528 2438 2493 1762 1942 2027
0
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803 ========== ======= ======= ======= ======== ======== ========
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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804
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805 **Gene Annotations:**
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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806 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
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807 information about the genes than just an ID number. The annotations will
14
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808 be available in the differential expression results table and the optional normalised counts table. They will also be used to generate interactive Glimma_ Volcano, MD plots and tables of differential expression. The input annotation file must contain a header row and have the gene IDs in the first column. The second column will be used to label the genes in the Volcano plot and interactive Glimma plots, additional columns will be available in the Glimma interactive table. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
0
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809
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810 Example:
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811
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812 ========== ========== ===================================================
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813 **GeneID** **Symbol** **GeneName**
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814 ---------- ---------- ---------------------------------------------------
4
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815 11287 Pzp pregnancy zone protein
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816 11298 Aanat arylalkylamine N-acetyltransferase
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817 11302 Aatk apoptosis-associated tyrosine kinase
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818 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
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819 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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820 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0
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821 ========== ========== ===================================================
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822
1
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823 **Factor Information:**
14
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824 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
1
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825
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826 Example:
0
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827
1
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828 ========== ============ =========
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829 **Sample** **Genotype** **Batch**
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830 ---------- ------------ ---------
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831 WT1 WT b1
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832 WT2 WT b2
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833 WT3 WT b3
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834 Mut1 Mut b1
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835 Mut2 Mut b2
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836 Mut3 Mut b3
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837 ========== ============ =========
0
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838
17
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839 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
3
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840
17
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841 *Groups:* The names of the groups for the factor. The names should only contain letters, numbers and underscores, other characters such as spaces and hyphens MUST not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. If the group names begin with a number an X will be added as a prefix.
1
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842
0
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843 **Contrasts of Interest:**
19
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844 The contrasts you wish to make between levels. A common contrast would be a simple difference between two levels: "Mut-WT"
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845 represents the difference between the mutant and wild type genotypes. Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. Alternatively, a tab-separated file can be input that has the names of the comparisons in the first column and one header row, as shown below.
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846
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847 Example:
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848
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849 ============= =
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850 **Contrasts**
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diff changeset
851 ------------- -
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852 Mut-WT
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parents: 18
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853 WT-Mut
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854 ============= =
0
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855
3
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856 **Filter Low Counts:**
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857 Genes with very low counts across all libraries provide little evidence for differential expression.
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858 In the biological point of view, a gene must be expressed at some minimal level before
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859 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
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860 pronounced discreteness of these counts interferes with some of the statistical approximations
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861 that are used later in the pipeline. These genes should be filtered out prior to further
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862 analysis.
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863 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
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864 for any of the conditions. Users can set their own definition of genes being expressed. Usually
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865 a gene is required to have a count of 5-10 in a library to be considered expressed in that
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866 library. Users should also filter with count-per-million (CPM) rather than filtering on the
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867 counts directly, as the latter does not account for differences in library sizes between samples.
0
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868
3
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869 Option to ignore the genes that do not show significant levels of
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870 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:
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871
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872 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
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873 least the number of samples specified under Minimum Samples.
0
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874
3
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875 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
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876 on Total Count or Minimum Samples.
0
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877
3
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878 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
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879 with a minimum total read count.
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880
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881 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
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882 requirement must be met in order for that gene to be kept.
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883
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diff changeset
884 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
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885 ensure that the sample requirement is appropriate. In the case of an experiment
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886 with two experimental groups each with two members, if there is a change from
3
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887 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
0
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888 then this will cause that gene to fail the criteria. When in doubt simply do not
3
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889 filter or consult the `limma User's Guide`_ for filtering recommendations.
0
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890
3
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891 **Advanced Options:**
0
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892
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893 By default error rate for multiple testing is controlled using Benjamini and
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894 Hochberg's false discovery rate control at a threshold value of 0.05. However
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895 there are options to change this to custom values.
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896
3
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897 * **Minimum log2-fold-change Required:**
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898 In addition to meeting the requirement for the adjusted statistic for
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899 multiple testing, the observation must have an absolute log2-fold-change
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900 greater than this threshold to be considered significant, thus highlighted
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901 in the MD plot.
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diff changeset
902
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903 * **Adjusted Threshold:**
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904 Set the threshold for the resulting value of the multiple testing control
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905 method. Only observations whose statistic falls below this value is
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906 considered significant, thus highlighted in the MD plot.
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907
0
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908 * **P-Value Adjustment Method:**
1
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909 Change the multiple testing control method, the options are BH(1995) and
0
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910 BY(2001) which are both false discovery rate controls. There is also
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911 Holm(1979) which is a method for family-wise error rate control.
1
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912
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913 **Testing relative to a threshold (TREAT):**
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914 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`_).
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diff changeset
915
3
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916 **Normalisation Method:**
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917 The most obvious technical factor that affects the read counts, other than gene expression
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diff changeset
918 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
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diff changeset
919 analysis for varying sequencing depths as represented by differing library sizes. This is
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920 part of the basic modeling procedure and flows automatically into fold-change or p-value
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921 calculations. It is always present, and doesn’t require any user intervention.
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922 The second most important technical influence on differential expression is one that is less
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923 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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924 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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925 This commonly becomes important when a small number of genes are very highly expressed
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926 in one sample, but not in another. The highly expressed genes can consume a substantial
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927 proportion of the total library size, causing the remaining genes to be under-sampled in that
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928 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
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929 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
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930
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931 **Robust Settings**
6
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932 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.
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933
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934 **Prior Count:**
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935 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`_.
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diff changeset
936
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diff changeset
937 **Apply Sample Weights:**
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diff changeset
938 If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still
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diff changeset
939 used in the statistical analysis but their impact is reduced. Use this
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diff changeset
940 whenever significant outliers are present. The MDS plotting tool in this package
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diff changeset
941 is useful for identifying outliers. For more information on this option see Liu et al. (2015).
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942
0
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diff changeset
943
1
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diff changeset
944 **Outputs**
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945
3
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diff changeset
946 This tool outputs
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diff changeset
947
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diff changeset
948 * a table of differentially expressed genes for each contrast of interest
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diff changeset
949 * a HTML report with plots and additional information
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parents: 2
diff changeset
950
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diff changeset
951 Optionally, under **Output Options** you can choose to output
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diff changeset
952
14
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diff changeset
953 * interactive Glimma plots and tables: MDS plot, and (if annotation file is input) Volcano plot and MD plot (default: Yes)
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diff changeset
954 * additional plots in the report and as PDFs
3
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diff changeset
955 * a normalised counts table
11
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parents: 10
diff changeset
956 * a library size information file
4
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diff changeset
957 * the R script used by this tool
3
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parents: 2
diff changeset
958 * an RData file
1
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diff changeset
959
0
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diff changeset
960 -----
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diff changeset
961
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diff changeset
962 **Citations:**
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diff changeset
963
3
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diff changeset
964 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
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diff changeset
965
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diff changeset
966 limma
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diff changeset
967
1
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diff changeset
968 Please cite the paper below for the limma software itself. Please also try
0
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diff changeset
969 to cite the appropriate methodology articles that describe the statistical
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diff changeset
970 methods implemented in limma, depending on which limma functions you are
3
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diff changeset
971 using. The methodology articles are listed in Section 2.1 of the `limma
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diff changeset
972 User's Guide`_.
0
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diff changeset
973
1
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diff changeset
974 * Smyth GK (2005). Limma: linear models for microarray data. In:
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diff changeset
975 'Bioinformatics and Computational Biology Solutions using R and
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diff changeset
976 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
0
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diff changeset
977 W. Huber (eds), Springer, New York, pages 397-420.
1
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978
0
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diff changeset
979 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:
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diff changeset
980 precision weights unlock linear model analysis tools for
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diff changeset
981 RNA-seq read counts. Genome Biology 15, R29.
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diff changeset
982
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diff changeset
983 * 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.
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diff changeset
984
1
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985 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
0
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diff changeset
986 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
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diff changeset
987 for microarray data. BMC Bioinformatics 7, Article 261.
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diff changeset
988
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989
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990 edgeR
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991
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992 Please cite the first paper for the software itself and the other papers for
1
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993 the various original statistical methods implemented in edgeR. See
3
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994 Section 1.2 in the `edgeR User's Guide`_ for more detail.
0
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995
1
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996 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
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997 package for differential expression analysis of digital gene expression
0
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998 data. Bioinformatics 26, 139-140
1
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diff changeset
999
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1000 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
0
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diff changeset
1001 differences in tag abundance. Bioinformatics 23, 2881-2887
1
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diff changeset
1002
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1003 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
0
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1004 binomial dispersion, with applications to SAGE data.
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1005 Biostatistics, 9, 321-332
1
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1006
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1007 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
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1008 of multifactor RNA-Seq experiments with respect to biological variation.
0
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1009 Nucleic Acids Research 40, 4288-4297
1
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1010
0
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1011 Please report problems or suggestions to: su.s@wehi.edu.au
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1012
3
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1013 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
9
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1014 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
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1015 .. _here: https://f1000research.com/articles/5-1408/v3
3
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1016 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
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1017 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
0
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1018 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
3
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1019 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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1020 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553
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1021 .. _Phipson et al. 2016: https://www.ncbi.nlm.nih.gov/pubmed/28367255
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1022 ]]></help>
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1023 <citations>
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1024 <citation type="doi">10.1186/gb-2014-15-2-r29</citation>
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1025 <citation type="doi">10.1093/nar/gkv412</citation>
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1026 </citations>
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1027 </tool>