Mercurial > repos > iuc > limma_voom

annotate limma_voom.xml @ 18:97e06a4c7c75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
author iuc
date Sun, 05 May 2019 09:02:04 -0400
parents 86b3df7db58b
children c9c6427edfe9
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18
97e06a4c7c75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
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1 <tool id="limma_voom" name="limma" version="3.38.3+galaxy2">
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>
1
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5
0
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6 <requirements>
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7 <requirement type="package" version="3.38.3">bioconductor-limma</requirement>
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8 <requirement type="package" version="3.24.1">bioconductor-edger</requirement>
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9 <requirement type="package" version="1.4.30">r-statmod</requirement>
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10 <requirement type="package" version="1.0.0">r-scales</requirement>
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11 <requirement type="package" version="0.2.20">r-rjson</requirement>
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12 <requirement type="package" version="1.20.2">r-getopt</requirement>
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13 <requirement type="package" version="3.0.1">r-gplots</requirement>
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14 <requirement type="package" version="1.10.0">bioconductor-glimma</requirement>
0
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15 </requirements>
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16
1
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17 <version_command><![CDATA[
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18 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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19 ]]></version_command>
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21 <command detect_errors="exit_code"><![CDATA[
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22 #import json
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23 Rscript '$__tool_directory__/limma_voom.R'
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25 -R '$outReport'
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26 -o '$outReport.files_path'
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28 #if $input.format=="files":
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30 ## Adapted from DESeq2 wrapper
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31 #set $temp_factor_names = list()
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32 #for $fact in $input.rep_factor:
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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33 #set $temp_factor = list()
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34 #for $g in $fact.rep_group:
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35 #set $count_files = list()
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36 #for $file in $g.countsFile:
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37 $count_files.append(str($file))
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38 #end for
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39 $temp_factor.append( {str($g.groupName): $count_files} )
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40 #end for
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41
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42 $temp_factor.reverse()
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43 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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44 #end for
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45 -j '#echo json.dumps(temp_factor_names)#'
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47 #elif $input.format=="matrix":
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48 -m '$input.counts'
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49 #if $input.fact.ffile=='yes':
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50 -f '$input.fact.finfo'
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51 #else:
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52 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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53 #end if
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54 #end if
1
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56 #if $anno.annoOpt=='yes':
3
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57 -a '$anno.geneanno'
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58 #end if
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59
3
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60 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
1
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61
3
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62 #if $f.filt.filt_select == 'yes':
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63 #if $f.filt.cformat.format_select == 'cpm':
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64 -c '$f.filt.cformat.cpmReq'
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65 -s '$f.filt.cformat.cpmSampleReq'
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66 #elif $f.filt.cformat.format_select == 'counts':
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67 -z '$f.filt.cformat.cntReq'
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68 #if $f.filt.cformat.samples.count_select == 'total':
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69 -y
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70 #elif $f.filt.cformat.samples.count_select == 'sample':
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71 -s '$f.filt.cformat.samples.cntSampleReq'
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72 #end if
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73 #end if
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74 #end if
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75
8
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76 #if $out.plots:
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77 -P $out.plots
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78 #end if
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79
12
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80 #if $out.filtCounts:
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81 -F
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82 #end if
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83
3
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84 #if $out.normCounts:
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85 -x
1
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86 #end if
0
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87
11
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88 #if $out.libinfo:
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89 -L
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90 #end if
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91
3
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92 #if $out.rdaOption:
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93 -r
1
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parents: 0
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94 #end if
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95
11
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96
3
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97 -l '$adv.lfc'
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98 -p '$adv.pVal'
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99 -d '$adv.pAdjust'
7
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100 -G '$adv.topgenes'
6
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101 #if $adv.treat:
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102 -T
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103 #end if
0
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104
3
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105 #if $deMethod.de_select == 'voom':
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106 #if $deMethod.weightOption:
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107 -w
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108 #end if
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109 #elif $deMethod.de_select == 'trend':
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110 -t $deMethod.prior_count
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111 #end if
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112
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113 -n '$adv.normalisationOption'
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114
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115 #if $adv.robOption:
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116 -b
1
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117 #end if
0
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118
1
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119 &&
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120 mkdir ./output_dir
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121
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122 &&
14
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123 cp '$outReport.files_path'/*tsv output_dir/
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124
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125 #if 'i' in str($out.plots).split( "," ):
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126 && cp -r ./glimma* '$outReport.files_path'
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127 #end if
13
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128
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129 #if $out.filtCounts or $out.normCounts:
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130 && cp '$outReport.files_path'/*counts output_dir/
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131 #end if
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132
4
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133 #if $out.rscript:
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134 && cp '$__tool_directory__/limma_voom.R' '$rscript'
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135 #end if
1
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136 ]]></command>
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137
0
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138 <inputs>
3
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139
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140 <!-- DE Method Option -->
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141 <conditional name="deMethod">
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142 <param name="de_select" type="select" label="Differential Expression Method" help="Select the limma-voom or limma-trend method. See Help section below for more information. Default: limma-voom">
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143 <option value="voom" selected="True">limma-voom</option>
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144 <option value="trend">limma-trend</option>
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145 </param>
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146 <when value="voom">
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147 <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality weights?"
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148 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False.">
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149 </param>
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150 </when>
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151 <when value="trend">
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152 <param name="prior_count" type="float" min="0" value="3" label="Prior count" help="Average count to be added to each observation to avoid taking log of zero. Default: 3." />
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153 </when>
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154 </conditional>
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155 <!-- Counts and Factors -->
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156 <conditional name="input">
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157 <param name="format" type="select" label="Count Files or Matrix?"
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158 help="You can choose to input either separate count files (one per sample) or a single count matrix">
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159 <option value="files">Separate Count Files</option>
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160 <option value="matrix">Single Count Matrix</option>
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161 </param>
1
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162
3
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163 <when value="files">
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164 <repeat name="rep_factor" title="Factor" min="1">
17
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165 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
3
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166 <sanitizer>
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167 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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168 </sanitizer>
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169 </param>
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170 <repeat name="rep_group" title="Group" min="2" default="2">
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171 <param name="groupName" type="text" label="Name"
17
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172 help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
3
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173 <sanitizer>
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174 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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175 </sanitizer>
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176 </param>
4
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177 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
3
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178 </repeat>
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179 </repeat>
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180 </when>
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181
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182 <when value="matrix">
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183 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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184
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185 <conditional name="fact">
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186 <param name="ffile" type="select" label="Input factor information from file?"
17
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187 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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188 <option value="no">No</option>
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189 <option value="yes">Yes</option>
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190 </param>
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191 <when value="yes">
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192 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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193 </when>
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194 <when value="no" >
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195 <repeat name="rep_factor" title="Factor" min="1">
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196 <param name="factorName" type="text" label="Factor Name"
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197 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
3
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198 <validator type="empty_field" />
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199 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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200 </param>
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201 <param name="groupNames" type="text" label="Groups"
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202 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
3
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203 <validator type="empty_field" />
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204 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
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205 </param>
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206 </repeat>
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207 </when>
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208 </conditional>
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209 </when>
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210 </conditional>
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211
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212 <!-- Gene Annotations -->
0
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213 <conditional name="anno">
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214 <param name="annoOpt" type="select" label="Use Gene Annotations?"
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215 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene, and used to label the top genes in the Volcano plot. Interactive Glimma Volcano and MD plots will also be generated. See Help section below.">
0
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216 <option value="no">No</option>
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217 <option value="yes">Yes</option>
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218 </param>
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219 <when value="yes">
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220 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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221 </when>
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222 <when value="no" />
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223 </conditional>
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224
3
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225 <!-- Contrasts -->
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226 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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227 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
3
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228 <validator type="empty_field" />
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229 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
0
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230 </param>
3
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231 </repeat>
1
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232
3
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233 <!-- Filter Options -->
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234 <section name="f" expanded="false" title="Filter Low Counts">
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235 <conditional name="filt">
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236 <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No">
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237 <option value="no" selected="true">No</option>
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238 <option value="yes">Yes</option>
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239 </param>
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240 <when value="yes">
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241 <conditional name="cformat">
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242 <param name="format_select" type="select" label="Filter on CPM or Count values?" help="It is slightly better to base the filtering on count-per-million (CPM) rather than the raw count values so as to avoid favoring genes expressed in samples sequenced to a higher depth. ">
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243 <option value="cpm">CPM</option>
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244 <option value="counts">Counts</option>
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245 </param>
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246 <when value="cpm">
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247 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/>
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248 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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249 help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
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250 </when>
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251 <when value="counts">
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252 <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information." />
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253 <conditional name="samples">
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254 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
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255 <option value="total">Total</option>
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256 <option value="sample">Sample</option>
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257 </param>
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258 <when value="total">
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259 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
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260 </when>
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261 <when value="sample">
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262 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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263 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/>
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264 </when>
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265 </conditional>
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266 </when>
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267 </conditional>
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268 </when>
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269 <when value="no" />
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270 </conditional>
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271 </section>
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272
3
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273 <!-- Output Options -->
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274 <section name="out" expanded="false" title="Output Options">
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275 <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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276 <option value="i" selected="True">Glimma Interactive Plots</option>
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277 <option value="d">Density Plots (if filtering)</option>
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278 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
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279 <option value="b">Box Plots (if normalising)</option>
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280 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
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281 <option value="m">MD Plots for individual samples</option>
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282 <option value="h">Heatmaps (top DE genes) </option>
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283 <option value="s">Stripcharts (top DE genes)</option>
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284 </param>
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285 <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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286 label="Output Filtered Counts Table?"
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287 help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
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288 </param>
3
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289 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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290 label="Output Normalised Counts Table?"
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291 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
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292 </param>
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293 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
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294 label="Output Library information file?"
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295 help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No">
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296 </param>
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297 <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"/>
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298 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
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299 label="Output RData file?"
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300 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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301 </param>
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302 </section>
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303
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304 <!-- Advanced Options -->
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305 <section name="adv" expanded="false" title="Advanced Options">
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306 <param name="lfc" type="float" value="0" min="0"
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307 label="Minimum Log2 Fold Change"
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308 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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309 <param name="pVal" type="float" value="0.05" min="0" max="1"
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310 label="P-Value Adjusted Threshold"
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311 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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312 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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313 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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314 <option value="BY">Benjamini and Yekutieli (2001)</option>
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315 <option value="holm">Holm (1979)</option>
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316 <option value="none">None</option>
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317 </param>
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318 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
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319 label="Test significance relative to a fold-change threshold (TREAT)"
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320 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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321 <param name="topgenes" type="integer" value="10" min="0" max="100"
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322 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
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323 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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324 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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325 <option value="TMM" selected="true">TMM</option>
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326 <option value="RLE">RLE</option>
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327 <option value="upperquartile">Upperquartile</option>
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328 <option value="none">None (Don't normalise)</option>
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329 </param>
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330 <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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331 </section>
0
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332
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333 </inputs>
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334
0
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335 <outputs>
1
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336 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
13
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337 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables">
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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338 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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339 </collection>
13
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340 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts">
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
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341 <filter>out['filtCounts']</filter>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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parents: 12
diff changeset
342 </data>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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parents: 12
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343 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts">
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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344 <filter>out['normCounts']</filter>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
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345 </data>
4
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parents: 3
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346 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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347 <filter>out['rscript']</filter>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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348 </data>
11
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349 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
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350 <filter>out['libinfo']</filter>
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
351 </data>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
352 </outputs>
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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353
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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354 <tests>
3
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parents: 2
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355 <!-- Ensure report is output -->
17
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iuc
parents: 16
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356 <test expect_num_outputs="2">
3
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parents: 2
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357 <param name="format" value="matrix" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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358 <param name="counts" value="matrix.txt" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
359 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
360 <param name="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
361 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
362 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
363 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
364 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
365 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
366 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
367 <param name="contrast" value="WT-Mut" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
368 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
369 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
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370 <param name="topgenes" value="6" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
371 <output_collection name="outTables" count="2">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
372 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
373 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
374 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
375 <has_text_matching expression="11304.*0.4573" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
376 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
377 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
378 <element name="limma-voom_WT-Mut" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
379 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
380 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
381 <has_text_matching expression="11304.*-0.4573" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
382 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
383 </element>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
384 </output_collection>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
385 <output name="outReport" >
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
386 <assert_contents>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
387 <has_text text="Limma Analysis Output" />
14
3133e833b3ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents: 13
diff changeset
388 <has_text text="Glimma Interactive Results" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
389 <not_has_text text="RData" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
390 </assert_contents>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
391 </output>
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
392 </test>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
393 <!-- Ensure annotation file input works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
394 <test expect_num_outputs="2">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
395 <param name="format" value="matrix" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
396 <param name="annoOpt" value="yes" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
397 <param name="geneanno" value="anno.txt" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
398 <param name="counts" value="matrix.txt" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
399 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
400 <param name="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
401 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
402 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
403 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
404 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
405 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
406 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
407 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
408 <output_collection name="outTables" count="1">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
409 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
410 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
411 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
412 <has_text_matching expression="11304.*Abca4.*0.4573" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
413 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
414 </element>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
415 </output_collection>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
416 </test>
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
417 <!-- Ensure Rscript and RData file can be output -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
418 <test expect_num_outputs="3">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
419 <param name="format" value="matrix" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
420 <param name="rscript" value="True"/>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
421 <param name="rdaOption" value="true" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
422 <param name="counts" value="matrix.txt" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
423 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
424 <param name="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
425 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
426 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
427 <repeat name="rep_contrast">
38aab66ae5cb 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="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
429 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
430 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
431 <param name="topgenes" value="6" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
432 <output name="outReport" >
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
433 <assert_contents>
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
434 <has_text text="RData" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
435 </assert_contents>
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
436 </output>
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
437 <output name="rscript">
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
438 <assert_contents>
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
439 <has_text_matching expression="Task run time" />
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
440 </assert_contents>
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
441 </output>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
442 </test>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
443 <!-- Ensure secondary factors work -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
444 <test expect_num_outputs="2">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
445 <param name="format" value="matrix" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
446 <param name="counts" value="matrix.txt" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
447 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
448 <param name="factorName" value="Genotype"/>
38aab66ae5cb 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="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
450 </repeat>
3
38aab66ae5cb 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">
38aab66ae5cb 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="Batch"/>
38aab66ae5cb 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="b1,b2,b3,b1,b2,b3"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
454 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
455 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
456 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
457 </repeat>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
458 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
459 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
460 <output_collection name="outTables" count="1" >
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
461 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
462 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
463 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
464 <has_text_matching expression="11304.*0.4590" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
465 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
466 </element>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
467 </output_collection>
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
468 </test>
14
3133e833b3ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents: 13
diff changeset
469 <!-- Ensure factors file with unordered samples works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
470 <test expect_num_outputs="2">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
471 <param name="format" value="matrix" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
472 <param name="ffile" value="yes" />
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
473 <param name="finfo" value="factorinfo.txt" />
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
474 <param name="counts" value="matrix.txt" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
475 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
476 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
477 </repeat>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
478 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
479 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
480 <output_collection name="outTables" count="1">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
481 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
482 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
483 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
484 <has_text_matching expression="11304.*0.4590" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
485 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
486 </element>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
487 </output_collection>
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
488 </test>
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
489 <!-- Ensure filtered and normalised count outputs works-->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
490 <test expect_num_outputs="4">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
491 <param name="format" value="matrix" />
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
492 <param name="filtCounts" value="true" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
493 <param name="normCounts" value="true" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
494 <param name="counts" value="matrix.txt" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
495 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
496 <param name="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
497 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
498 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
499 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
500 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
501 </repeat>
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
502 <param name="filt_select" value="yes" />
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
503 <param name="format_select" value="counts"/>
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
504 <param name="cntReq" value="10"/>
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
505 <param name="count_select" value="sample"/>
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
506 <param name="cntSampleReq" value="3"/>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
507 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
508 <param name="topgenes" value="6" />
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
509 <output_collection name="outTables" count="1">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
510 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
511 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
512 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
513 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
514 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
515 </element>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
516 </output_collection>
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
517 <output name="outNorm" ftype="tabular" >
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
518 <assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
519 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
520 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
521 </assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
522 </output>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
523 <output name="outFilt" ftype="tabular" >
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
524 <assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
525 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
526 <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
527 <not_has_text text="11302"/>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
528 </assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
529 </output>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
530 </test>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
531 <!-- Ensure multiple counts files input works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
532 <test expect_num_outputs="3">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
533 <param name="format" value="files" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
534 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
535 <param name="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
536 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
537 <param name="groupName" value="WT"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
538 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
539 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
540 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
541 <param name="groupName" value="Mut"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
542 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
543 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
544 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
545 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
546 <param name="factorName" value="Batch"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
547 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
548 <param name="groupName" value="b1"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
549 <param name="countsFile" value="WT1.counts,Mut1.counts"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
550 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
551 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
552 <param name="groupName" value="b2"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
553 <param name="countsFile" value="WT2.counts,Mut2.counts"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
554 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
555 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
556 <param name="groupName" value="b3"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
557 <param name="countsFile" value="WT3.counts,Mut3.counts"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
558 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
559 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
560 <param name="annoOpt" value="yes" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
561 <param name="geneanno" value="anno.txt" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
562 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
563 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
564 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
565 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
566 <param name="contrast" value="WT-Mut" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
567 </repeat>
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
568 <param name="topgenes" value="6" />
3
38aab66ae5cb 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="normCounts" value="true" />
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
570 <output_collection name="outTables" count="2">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
571 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
572 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
573 <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
574 <has_text_matching expression="11304.*Abca4.*0.4590" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
575 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
576 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
577 <element name="limma-voom_WT-Mut" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
578 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
579 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
580 <has_text_matching expression="11304.*Abca4.*-0.4590" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
581 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
582 </element>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
583 </output_collection>
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
584 <output name="outNorm" ftype="tabular" >
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
585 <assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
586 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
587 <has_text_matching expression="11304.*Abca4.*15.7545" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
588 </assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
589 </output>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
590 </test>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
591 <!-- Ensure limma-trend option works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
592 <test expect_num_outputs="2">
3
38aab66ae5cb 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="format" value="matrix" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
594 <param name="counts" value="matrix.txt" />
38aab66ae5cb 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_factor">
38aab66ae5cb 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="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
597 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
598 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
599 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
600 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
601 </repeat>
38aab66ae5cb 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="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
603 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
604 <param name="de_select" value="trend" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
605 <output name="outReport" >
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
606 <assert_contents>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
607 <has_text text="The limma-trend method was used" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
608 </assert_contents>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
609 </output>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
610 <output_collection name="outTables" count="1">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
611 <element name="limma-trend_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
612 <assert_contents>
a61a6e62e91f 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="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
614 <has_text_matching expression="11304.*0.4540" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
615 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
616 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
617 </output_collection>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
618 </test>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
619 <!-- Ensure limma-trend option with annotation works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
620 <test expect_num_outputs="2">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
621 <param name="format" value="matrix" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
622 <param name="counts" value="matrix.txt" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
623 <param name="annoOpt" value="yes" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
624 <param name="geneanno" value="anno.txt" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
625 <repeat name="rep_factor">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
626 <param name="factorName" value="Genotype"/>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
627 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
628 </repeat>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
629 <repeat name="rep_contrast">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
630 <param name="contrast" value="Mut-WT" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
631 </repeat>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
632 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
633 <param name="topgenes" value="6" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
634 <param name="de_select" value="trend" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
635 <output name="outReport" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
636 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
637 <has_text text="The limma-trend method was used" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
638 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
639 </output>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
640 <output_collection name="outTables" count="1">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
641 <element name="limma-trend_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
642 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
643 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
644 <has_text_matching expression="11304.*0.4540" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
645 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
646 </element>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
647 </output_collection>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
648 </test>
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
649 <!-- Ensure samples and groups beginning with numbers can be handled -->
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
650 <test expect_num_outputs="3">
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
651 <param name="format" value="matrix" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
652 <param name="counts" value="matrix_num.txt" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
653 <param name="annoOpt" value="yes" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
654 <param name="geneanno" value="anno.txt" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
655 <repeat name="rep_factor">
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
656 <param name="factorName" value="Group"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
657 <param name="groupNames" value="2,2,2,1,1,1" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
658 </repeat>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
659 <repeat name="rep_contrast">
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
660 <param name="contrast" value="2-1" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
661 </repeat>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
662 <param name="filt_select" value="yes" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
663 <param name="format_select" value="counts"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
664 <param name="cntReq" value="10"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
665 <param name="count_select" value="sample"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
666 <param name="cntSampleReq" value="3"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
667 <param name="normalisationOption" value="TMM" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
668 <param name="normCounts" value="true" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
669 <param name="topgenes" value="6" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
670 <param name="de_select" value="voom" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
671 <output_collection name="outTables" count="1">
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
672 <element name="limma-voom_X2-X1" ftype="tabular" >
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
673 <assert_contents>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
674 <has_text_matching expression="EntrezID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
675 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
676 </assert_contents>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
677 </element>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
678 </output_collection>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
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diff changeset
679 <output name="outNorm" ftype="tabular" >
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680 <assert_contents>
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681 <has_text_matching expression="EntrezID.*2-1.*2-2.*2-3.*1-1.*1-2.*1-3" />
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682 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
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683 </assert_contents>
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684 </output>
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685 </test>
0
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686 </tests>
1
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687
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688 <help><![CDATA[
0
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689 .. class:: infomark
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690
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691 **What it does**
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692
14
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693 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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694
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695 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
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696
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697 -----
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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698
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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699 **Inputs**
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700
3
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701 **Differential Expression Method:**
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702 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom.
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703 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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704 robust approach to differential expression is to use limma-trend. This approach will usually work well if the
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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705 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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706
0
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707 **Counts Data:**
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708 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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diff changeset
709
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diff changeset
710 Example - **Separate Count Files**:
0
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diff changeset
711
3
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parents: 2
diff changeset
712 ========== =======
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diff changeset
713 **GeneID** **WT1**
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diff changeset
714 ---------- -------
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diff changeset
715 11287 1699
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iuc
parents: 2
diff changeset
716 11298 1905
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parents: 2
diff changeset
717 11302 6
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
718 11303 2099
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
719 11304 356
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diff changeset
720 11305 2528
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iuc
parents: 2
diff changeset
721 ========== =======
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iuc
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diff changeset
722
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
723 Example - **Single Count Matrix**:
0
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iuc
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diff changeset
724
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
725 ========== ======= ======= ======= ======== ======== ========
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
726 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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727 ---------- ------- ------- ------- -------- -------- --------
1
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parents: 0
diff changeset
728 11287 1699 1528 1601 1463 1441 1495
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iuc
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diff changeset
729 11298 1905 1744 1834 1345 1291 1346
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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diff changeset
730 11302 6 8 7 5 6 5
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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diff changeset
731 11303 2099 1974 2100 1574 1519 1654
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diff changeset
732 11304 356 312 337 361 397 346
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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diff changeset
733 11305 2528 2438 2493 1762 1942 2027
0
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734 ========== ======= ======= ======= ======== ======== ========
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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735
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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736 **Gene Annotations:**
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
737 Optional input for gene annotations, this can contain more
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
738 information about the genes than just an ID number. The annotations will
14
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diff changeset
739 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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diff changeset
740
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
741 Example:
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742
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743 ========== ========== ===================================================
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744 **GeneID** **Symbol** **GeneName**
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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745 ---------- ---------- ---------------------------------------------------
4
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diff changeset
746 11287 Pzp pregnancy zone protein
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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747 11298 Aanat arylalkylamine N-acetyltransferase
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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748 11302 Aatk apoptosis-associated tyrosine kinase
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749 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
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750 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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751 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0
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752 ========== ========== ===================================================
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753
1
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754 **Factor Information:**
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755 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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756
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757 Example:
0
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758
1
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759 ========== ============ =========
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diff changeset
760 **Sample** **Genotype** **Batch**
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761 ---------- ------------ ---------
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diff changeset
762 WT1 WT b1
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763 WT2 WT b2
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parents: 0
diff changeset
764 WT3 WT b3
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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parents: 0
diff changeset
765 Mut1 Mut b1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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parents: 0
diff changeset
766 Mut2 Mut b2
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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parents: 0
diff changeset
767 Mut3 Mut b3
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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parents: 0
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768 ========== ============ =========
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
769
17
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diff changeset
770 *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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parents: 2
diff changeset
771
17
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diff changeset
772 *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
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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diff changeset
773
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
774 **Contrasts of Interest:**
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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775 The contrasts you wish to make between levels.
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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776 A common contrast would be a simple difference between two levels: "Mut-WT"
0
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diff changeset
777 represents the difference between the mutant and wild type genotypes.
3
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778 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
779
3
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parents: 2
diff changeset
780 **Filter Low Counts:**
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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781 Genes with very low counts across all libraries provide little evidence for differential expression.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
782 In the biological point of view, a gene must be expressed at some minimal level before
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
783 it is likely to be translated into a protein or to be biologically important. In addition, the
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
diff changeset
784 pronounced discreteness of these counts interferes with some of the statistical approximations
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
785 that are used later in the pipeline. These genes should be filtered out prior to further
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
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786 analysis.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
787 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
788 for any of the conditions. Users can set their own definition of genes being expressed. Usually
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
789 a gene is required to have a count of 5-10 in a library to be considered expressed in that
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
790 library. Users should also filter with count-per-million (CPM) rather than filtering on the
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
791 counts directly, as the latter does not account for differences in library sizes between samples.
0
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792
3
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diff changeset
793 Option to ignore the genes that do not show significant levels of
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
794 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:
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
795
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
796 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
797 least the number of samples specified under Minimum Samples.
0
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798
3
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diff changeset
799 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
800 on Total Count or Minimum Samples.
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
801
3
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diff changeset
802 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
803 with a minimum total read count.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
diff changeset
804
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diff changeset
805 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
806 requirement must be met in order for that gene to be kept.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
807
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
808 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
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
809 ensure that the sample requirement is appropriate. In the case of an experiment
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
810 with two experimental groups each with two members, if there is a change from
3
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diff changeset
811 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
0
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diff changeset
812 then this will cause that gene to fail the criteria. When in doubt simply do not
3
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diff changeset
813 filter or consult the `limma User's Guide`_ for filtering recommendations.
0
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814
3
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diff changeset
815 **Advanced Options:**
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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816
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817 By default error rate for multiple testing is controlled using Benjamini and
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
818 Hochberg's false discovery rate control at a threshold value of 0.05. However
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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819 there are options to change this to custom values.
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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820
3
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821 * **Minimum log2-fold-change Required:**
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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822 In addition to meeting the requirement for the adjusted statistic for
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
823 multiple testing, the observation must have an absolute log2-fold-change
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
824 greater than this threshold to be considered significant, thus highlighted
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
825 in the MD plot.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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826
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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827 * **Adjusted Threshold:**
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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828 Set the threshold for the resulting value of the multiple testing control
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
829 method. Only observations whose statistic falls below this value is
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
830 considered significant, thus highlighted in the MD plot.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
831
0
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832 * **P-Value Adjustment Method:**
1
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833 Change the multiple testing control method, the options are BH(1995) and
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
834 BY(2001) which are both false discovery rate controls. There is also
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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835 Holm(1979) which is a method for family-wise error rate control.
1
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836
6
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diff changeset
837 **Testing relative to a threshold (TREAT):**
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838 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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839
3
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diff changeset
840 **Normalisation Method:**
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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841 The most obvious technical factor that affects the read counts, other than gene expression
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
842 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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843 analysis for varying sequencing depths as represented by differing library sizes. This is
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
844 part of the basic modeling procedure and flows automatically into fold-change or p-value
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
845 calculations. It is always present, and doesn’t require any user intervention.
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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846 The second most important technical influence on differential expression is one that is less
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
847 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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848 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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849 This commonly becomes important when a small number of genes are very highly expressed
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850 in one sample, but not in another. The highly expressed genes can consume a substantial
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diff changeset
851 proportion of the total library size, causing the remaining genes to be under-sampled in that
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diff changeset
852 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
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853 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`_.
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854
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855 **Robust Settings**
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856 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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857
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858 **Prior Count:**
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859 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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860
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861 **Apply Sample Weights:**
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862 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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863 used in the statistical analysis but their impact is reduced. Use this
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864 whenever significant outliers are present. The MDS plotting tool in this package
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diff changeset
865 is useful for identifying outliers. For more information on this option see Liu et al. (2015).
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866
0
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867
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868 **Outputs**
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869
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870 This tool outputs
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871
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872 * a table of differentially expressed genes for each contrast of interest
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873 * a HTML report with plots and additional information
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874
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875 Optionally, under **Output Options** you can choose to output
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876
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877 * interactive Glimma plots and tables: MDS plot, and (if annotation file is input) Volcano plot and MD plot (default: Yes)
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878 * additional plots in the report and as PDFs
3
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879 * a normalised counts table
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880 * a library size information file
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881 * the R script used by this tool
3
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882 * an RData file
1
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883
0
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884 -----
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885
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886 **Citations:**
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887
3
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888 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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889
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diff changeset
890 limma
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891
1
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892 Please cite the paper below for the limma software itself. Please also try
0
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893 to cite the appropriate methodology articles that describe the statistical
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894 methods implemented in limma, depending on which limma functions you are
3
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diff changeset
895 using. The methodology articles are listed in Section 2.1 of the `limma
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896 User's Guide`_.
0
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897
1
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898 * Smyth GK (2005). Limma: linear models for microarray data. In:
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899 'Bioinformatics and Computational Biology Solutions using R and
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diff changeset
900 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
0
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901 W. Huber (eds), Springer, New York, pages 397-420.
1
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902
0
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diff changeset
903 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:
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diff changeset
904 precision weights unlock linear model analysis tools for
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diff changeset
905 RNA-seq read counts. Genome Biology 15, R29.
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diff changeset
906
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diff changeset
907 * 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
908
1
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909 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
0
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910 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
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911 for microarray data. BMC Bioinformatics 7, Article 261.
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diff changeset
912
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913
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914 edgeR
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915
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916 Please cite the first paper for the software itself and the other papers for
1
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917 the various original statistical methods implemented in edgeR. See
3
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918 Section 1.2 in the `edgeR User's Guide`_ for more detail.
0
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919
1
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920 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
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921 package for differential expression analysis of digital gene expression
0
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922 data. Bioinformatics 26, 139-140
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diff changeset
923
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924 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
0
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925 differences in tag abundance. Bioinformatics 23, 2881-2887
1
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diff changeset
926
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927 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
0
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928 binomial dispersion, with applications to SAGE data.
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929 Biostatistics, 9, 321-332
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930
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931 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
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932 of multifactor RNA-Seq experiments with respect to biological variation.
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933 Nucleic Acids Research 40, 4288-4297
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934
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935 Please report problems or suggestions to: su.s@wehi.edu.au
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936
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937 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
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938 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
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939 .. _here: https://f1000research.com/articles/5-1408/v3
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940 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
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941 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
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942 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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943 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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944 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553
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945 .. _Phipson et al. 2016: https://www.ncbi.nlm.nih.gov/pubmed/28367255
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946 ]]></help>
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947 <citations>
3
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948 <citation type="doi">10.1186/gb-2014-15-2-r29</citation>
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949 <citation type="doi">10.1093/nar/gkv412</citation>
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950 </citations>
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951 </tool>