Mercurial > repos > iuc > limma_voom

annotate limma_voom.xml @ 5:d8a55b5f0de0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
author iuc
date Sat, 05 May 2018 17:55:13 -0400
parents a61a6e62e91f
children 39fa12a6d885
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5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
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1 <tool id="limma_voom" name="limma" version="3.34.9.1">
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="3.34.9">bioconductor-limma</requirement>
3
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8 <requirement type="package" version="3.20.7">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="0.5.0">r-scales</requirement>
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11 <requirement type="package" version="0.2.15">r-rjson</requirement>
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12 <requirement type="package" version="1.20.0">r-getopt</requirement>
0
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13 </requirements>
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14
1
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15 <version_command><![CDATA[
3
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16 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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
1
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17 ]]></version_command>
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19 <command detect_errors="exit_code"><![CDATA[
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20 #import json
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21 Rscript '$__tool_directory__/limma_voom.R'
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22
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23 -R '$outReport'
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24 -o '$outReport.files_path'
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26 #if $input.format=="files":
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27
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28 ## Adapted from DESeq2 wrapper
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29 #set $temp_factor_names = list()
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30 #for $fact in $input.rep_factor:
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31 #set $temp_factor = list()
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32 #for $g in $fact.rep_group:
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33 #set $count_files = list()
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34 #for $file in $g.countsFile:
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35 $count_files.append(str($file))
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36 #end for
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37 $temp_factor.append( {str($g.groupName): $count_files} )
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38 #end for
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39
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40 $temp_factor.reverse()
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41 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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42 #end for
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43 -j '#echo json.dumps(temp_factor_names)#'
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44
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45 #elif $input.format=="matrix":
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46 -m '$input.counts'
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47 #if $input.fact.ffile=='yes':
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48 -f '$input.fact.finfo'
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49 #else:
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50 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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51 #end if
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52 #end if
1
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54 #if $anno.annoOpt=='yes':
3
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55 -a '$anno.geneanno'
1
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56 #end if
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57
3
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58 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
1
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59
3
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60 #if $f.filt.filt_select == 'yes':
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61 #if $f.filt.cformat.format_select == 'cpm':
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62 -c '$f.filt.cformat.cpmReq'
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63 -s '$f.filt.cformat.cpmSampleReq'
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64 #elif $f.filt.cformat.format_select == 'counts':
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65 -z '$f.filt.cformat.cntReq'
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66 #if $f.filt.cformat.samples.count_select == 'total':
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67 -y
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68 #elif $f.filt.cformat.samples.count_select == 'sample':
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69 -s '$f.filt.cformat.samples.cntSampleReq'
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70 #end if
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71 #end if
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72 #end if
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73
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74 #if $out.normCounts:
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75 -x
1
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76 #end if
0
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77
3
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78 #if $out.rdaOption:
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79 -r
1
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80 #end if
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81
3
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82 -l '$adv.lfc'
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83 -p '$adv.pVal'
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84 -d '$adv.pAdjust'
0
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85
3
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86 #if $deMethod.de_select == 'voom':
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87 #if $deMethod.weightOption:
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88 -w
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89 #end if
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90 #elif $deMethod.de_select == 'trend':
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91 -t $deMethod.prior_count
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92 #end if
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93
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94 -n '$adv.normalisationOption'
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95
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96 #if $adv.robOption:
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97 -b
1
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98 #end if
0
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99
1
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100 &&
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101 mkdir ./output_dir
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102
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103 &&
2
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104 cp '$outReport.files_path'/*.tsv output_dir/
4
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105
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106 #if $out.rscript:
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107 && cp '$__tool_directory__/limma_voom.R' '$rscript'
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108 #end if
1
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109 ]]></command>
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110
0
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111 <inputs>
3
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112
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113 <!-- DE Method Option -->
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114 <conditional name="deMethod">
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115 <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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116 <option value="voom" selected="True">limma-voom</option>
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117 <option value="trend">limma-trend</option>
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118 </param>
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119 <when value="voom">
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120 <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality weights?"
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121 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False.">
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122 </param>
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123 </when>
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124 <when value="trend">
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125 <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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126 </when>
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127 </conditional>
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128 <!-- Counts and Factors -->
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129 <conditional name="input">
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130 <param name="format" type="select" label="Count Files or Matrix?"
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131 help="You can choose to input either separate count files (one per sample) or a single count matrix">
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132 <option value="files">Separate Count Files</option>
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133 <option value="matrix">Single Count Matrix</option>
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134 </param>
1
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135
3
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136 <when value="files">
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137 <repeat name="rep_factor" title="Factor" min="1">
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138 <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.">
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139 <sanitizer>
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140 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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141 </sanitizer>
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142 </param>
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143 <repeat name="rep_group" title="Group" min="2" default="2">
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144 <param name="groupName" type="text" label="Name"
4
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145 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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146 <sanitizer>
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147 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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148 </sanitizer>
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149 </param>
4
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150 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
3
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151 </repeat>
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152 </repeat>
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153 </when>
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154
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155 <when value="matrix">
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156 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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157
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158 <conditional name="fact">
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159 <param name="ffile" type="select" label="Input factor information from file?"
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160 help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
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161 <option value="no">No</option>
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162 <option value="yes">Yes</option>
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163 </param>
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164 <when value="yes">
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165 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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166 </when>
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167 <when value="no" >
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168 <repeat name="rep_factor" title="Factor" min="1">
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169 <param name="factorName" type="text" label="Factor Name"
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170 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.">
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171 <validator type="empty_field" />
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172 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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173 </param>
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174 <param name="groupNames" type="text" label="Groups"
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175 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).">
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176 <validator type="empty_field" />
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177 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
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178 </param>
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179 </repeat>
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180 </when>
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181 </conditional>
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182 </when>
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183 </conditional>
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184
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185 <!-- Gene Annotations -->
0
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186 <conditional name="anno">
1
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187 <param name="annoOpt" type="select" label="Use Gene Annotations?"
3
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188 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. See Help section below.">
0
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189 <option value="no">No</option>
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190 <option value="yes">Yes</option>
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191 </param>
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192 <when value="yes">
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193 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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194 </when>
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195 <when value="no" />
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196 </conditional>
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197
3
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198 <!-- Contrasts -->
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199 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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200 <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 more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
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201 <validator type="empty_field" />
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202 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
0
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203 </param>
3
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204 </repeat>
1
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205
3
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206 <!-- Filter Options -->
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207 <section name="f" expanded="false" title="Filter Low Counts">
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208 <conditional name="filt">
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209 <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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210 <option value="no" selected="true">No</option>
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211 <option value="yes">Yes</option>
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212 </param>
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213 <when value="yes">
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214 <conditional name="cformat">
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215 <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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216 <option value="cpm">CPM</option>
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217 <option value="counts">Counts</option>
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218 </param>
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219 <when value="cpm">
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220 <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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221 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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222 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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223 </when>
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224 <when value="counts">
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225 <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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226 <conditional name="samples">
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227 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
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228 <option value="total">Total</option>
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229 <option value="sample">Sample</option>
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230 </param>
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231 <when value="total">
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232 <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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233 </when>
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234 <when value="sample">
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235 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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236 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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237 </when>
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238 </conditional>
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239 </when>
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240 </conditional>
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241 </when>
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242 <when value="no" />
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243 </conditional>
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244 </section>
1
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245
3
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246 <!-- Output Options -->
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247 <section name="out" expanded="false" title="Output Options">
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248 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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249 label="Output Normalised Counts Table?"
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250 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
1
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251 </param>
4
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252 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
3
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253 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
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254 label="Output RData file?"
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255 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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256 </param>
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257 </section>
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258
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259 <!-- Advanced Options -->
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260 <section name="adv" expanded="false" title="Advanced Options">
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261 <param name="lfc" type="float" value="0" min="0"
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262 label="Minimum Log2 Fold Change"
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263 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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264 <param name="pVal" type="float" value="0.05" min="0" max="1"
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265 label="P-Value Adjusted Threshold"
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266 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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267 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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268 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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269 <option value="BY">Benjamini and Yekutieli (2001)</option>
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270 <option value="holm">Holm (1979)</option>
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271 <option value="none">None</option>
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272 </param>
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273 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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274 <option value="TMM" selected="true">TMM</option>
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275 <option value="RLE">RLE</option>
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276 <option value="upperquartile">Upperquartile</option>
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277 <option value="none">None (Don't normalise)</option>
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278 </param>
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279 <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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280 </section>
0
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281
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282 </inputs>
1
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283
0
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284 <outputs>
1
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285 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
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286 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
0
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287 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
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288 </collection>
4
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289 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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290 <filter>out['rscript']</filter>
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291 </data>
0
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292 </outputs>
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293
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294 <tests>
3
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295 <!-- Ensure report is output -->
0
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296 <test>
3
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297 <param name="format" value="matrix" />
0
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298 <param name="counts" value="matrix.txt" />
3
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299 <repeat name="rep_factor">
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300 <param name="factorName" value="Genotype"/>
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301 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
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302 </repeat>
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303 <repeat name="rep_contrast">
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304 <param name="contrast" value="Mut-WT" />
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305 </repeat>
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306 <repeat name="rep_contrast">
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307 <param name="contrast" value="WT-Mut" />
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308 </repeat>
0
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309 <param name="normalisationOption" value="TMM" />
1
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310 <output_collection name="outTables" count="2">
4
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311 <element name="limma-voom_Mut-WT" ftype="tabular" >
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312 <assert_contents>
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313 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
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314 <has_text_matching expression="11304.*0.4573" />
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315 </assert_contents>
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316 </element>
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317 <element name="limma-voom_WT-Mut" ftype="tabular" >
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318 <assert_contents>
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319 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
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320 <has_text_matching expression="11304.*-0.4573" />
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321 </assert_contents>
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322 </element>
1
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323 </output_collection>
0
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324 <output name="outReport" >
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325 <assert_contents>
3
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326 <has_text text="Limma Analysis Output" />
0
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327 <not_has_text text="RData" />
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328 </assert_contents>
1
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329 </output>
4
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330 </test>
3
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331 <!-- Ensure annotation file input works -->
0
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332 <test>
3
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333 <param name="format" value="matrix" />
0
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334 <param name="annoOpt" value="yes" />
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335 <param name="geneanno" value="anno.txt" />
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336 <param name="counts" value="matrix.txt" />
3
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337 <repeat name="rep_factor">
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338 <param name="factorName" value="Genotype"/>
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339 <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
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340 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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341 <repeat name="rep_contrast">
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iuc
parents: 2
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342 <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
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343 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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344 <param name="normalisationOption" value="TMM" />
3
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345 <output_collection name="outTables" count="1">
4
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iuc
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346 <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
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347 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
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348 <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
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349 <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
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350 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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351 </element>
1
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iuc
parents: 0
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352 </output_collection>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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353 </test>
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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354 <!-- Ensure Rscript and RData file can be output -->
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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355 <test>
3
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iuc
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356 <param name="format" value="matrix" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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357 <param name="rscript" value="True"/>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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358 <param name="rdaOption" value="true" />
1
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359 <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
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360 <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
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361 <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
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362 <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
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363 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
364 <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
365 <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
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366 </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
367 <param name="normalisationOption" value="TMM" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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368 <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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369 <assert_contents>
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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370 <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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371 </assert_contents>
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
372 </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
373 <output name="rscript" value="out_rscript.txt"/>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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374 </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
375 <!-- Ensure secondary factors work -->
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
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376 <test>
3
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iuc
parents: 2
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377 <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
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378 <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
379 <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
380 <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
381 <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
382 </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
383 <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
384 <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
385 <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
386 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
387 <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
388 <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
389 </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
390 <param name="normalisationOption" value="TMM" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
391 <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
392 <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
393 <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
394 <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
395 <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
396 </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
397 </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
398 </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
399 </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
400 <!-- Ensure factors file input works -->
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
401 <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
402 <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
403 <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
404 <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
405 <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
406 <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
407 <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
408 </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
409 <param name="normalisationOption" value="TMM" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
410 <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
411 <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
412 <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
413 <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
414 <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
415 </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
416 </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
417 </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
418 </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
419 <!-- Ensure normalised counts file output works-->
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
420 <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
421 <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
422 <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
423 <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
424 <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
425 <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
426 <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
427 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
428 <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
429 <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
430 </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
431 <param name="normalisationOption" value="TMM" />
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
432 <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
433 <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
434 <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
435 <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
436 <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
437 </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
438 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
439 <element name="limma-voom_normcounts" 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
440 <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
441 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
442 <has_text_matching expression="11304.*15.7545" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
443 </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
444 </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
445 </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
446 </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
447 <!-- Ensure multiple counts files input works -->
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
448 <test>
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="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
450 <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
451 <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
452 <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
453 <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
454 <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
455 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
456 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
457 <param name="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
458 <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
459 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
460 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
461 <repeat name="rep_factor">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
462 <param name="factorName" value="Batch"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
463 <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
464 <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
465 <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
466 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
467 <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
468 <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
469 <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
470 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
471 <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
472 <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
473 <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
474 </repeat>
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>
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="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
477 <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
478 <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
479 <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
480 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
481 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
482 <param name="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
483 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
484 <param name="normCounts" value="true" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
485 <output_collection name="outTables" count="3">
4
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 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
487 <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
488 <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
489 <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
490 </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
491 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
492 <element name="limma-voom_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
493 <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
494 <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
495 <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
496 </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
497 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
498 <element name="limma-voom_normcounts" 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
499 <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
500 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
501 <has_text_matching expression="11304.*Abca4.*15.7545" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
502 </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
503 </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
504 </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
505 </test>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
506 <!-- Ensure limma-trend option works -->
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
507 <test>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
508 <param name="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
509 <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
510 <repeat name="rep_factor">
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
511 <param name="factorName" value="Genotype"/>
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diff changeset
512 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
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diff changeset
513 </repeat>
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iuc
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diff changeset
514 <repeat name="rep_contrast">
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515 <param name="contrast" value="Mut-WT" />
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diff changeset
516 </repeat>
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517 <param name="normalisationOption" value="TMM" />
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518 <param name="de_select" value="trend" />
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519 <param name="rdaOption" value="true" />
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520 <output name="outReport" >
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521 <assert_contents>
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522 <has_text text="The limma-trend method was used" />
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523 </assert_contents>
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524 </output>
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525 <output_collection name="outTables" count="1">
4
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526 <element name="limma-trend_Mut-WT" ftype="tabular" >
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527 <assert_contents>
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528 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
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529 <has_text_matching expression="11304.*0.4540" />
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530 </assert_contents>
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diff changeset
531 </element>
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532 </output_collection>
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533 </test>
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534 <!-- Ensure limma-trend option with annotation works -->
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535 <test>
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536 <param name="format" value="matrix" />
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537 <param name="counts" value="matrix.txt" />
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538 <param name="annoOpt" value="yes" />
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539 <param name="geneanno" value="anno.txt" />
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540 <repeat name="rep_factor">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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541 <param name="factorName" value="Genotype"/>
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542 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
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543 </repeat>
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544 <repeat name="rep_contrast">
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545 <param name="contrast" value="Mut-WT" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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546 </repeat>
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547 <param name="normalisationOption" value="TMM" />
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548 <param name="de_select" value="trend" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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549 <param name="rdaOption" value="true" />
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550 <output name="outReport" >
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551 <assert_contents>
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552 <has_text text="The limma-trend method was used" />
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553 </assert_contents>
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554 </output>
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555 <output_collection name="outTables" count="1">
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556 <element name="limma-trend_Mut-WT" ftype="tabular" >
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557 <assert_contents>
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558 <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
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559 <has_text_matching expression="11304.*0.4540" />
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560 </assert_contents>
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561 </element>
3
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562 </output_collection>
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563 </test>
0
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564 </tests>
1
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565
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566 <help><![CDATA[
0
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567 .. class:: infomark
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568
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569 **What it does**
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570
3
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571 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis.
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572
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573 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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574
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575 -----
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576
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577 **Inputs**
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578
3
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diff changeset
579 **Differential Expression Method:**
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580 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom.
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581 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most
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diff changeset
582 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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diff changeset
583 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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diff changeset
584
0
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585 **Counts Data:**
3
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586 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
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diff changeset
587
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588 Example - **Separate Count Files**:
0
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diff changeset
589
3
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diff changeset
590 ========== =======
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diff changeset
591 **GeneID** **WT1**
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592 ---------- -------
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diff changeset
593 11287 1699
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diff changeset
594 11298 1905
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diff changeset
595 11302 6
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diff changeset
596 11303 2099
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597 11304 356
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598 11305 2528
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599 ========== =======
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600
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601 Example - **Single Count Matrix**:
0
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602
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603 ========== ======= ======= ======= ======== ======== ========
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604 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
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605 ---------- ------- ------- ------- -------- -------- --------
1
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606 11287 1699 1528 1601 1463 1441 1495
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607 11298 1905 1744 1834 1345 1291 1346
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608 11302 6 8 7 5 6 5
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609 11303 2099 1974 2100 1574 1519 1654
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610 11304 356 312 337 361 397 346
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611 11305 2528 2438 2493 1762 1942 2027
0
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612 ========== ======= ======= ======= ======== ======== ========
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613
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614 **Gene Annotations:**
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615 Optional input for gene annotations, this can contain more
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616 information about the genes than just an ID number. The annotations will
4
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617 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. 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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618
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619 Example:
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620
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621 ========== ========== ===================================================
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622 **GeneID** **Symbol** **GeneName**
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623 ---------- ---------- ---------------------------------------------------
4
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624 11287 Pzp pregnancy zone protein
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625 11298 Aanat arylalkylamine N-acetyltransferase
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626 11302 Aatk apoptosis-associated tyrosine kinase
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627 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
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628 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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629 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0
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630 ========== ========== ===================================================
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631
1
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632 **Factor Information:**
3
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633 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
1
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634
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635 Example:
0
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636
1
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637 ========== ============ =========
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638 **Sample** **Genotype** **Batch**
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639 ---------- ------------ ---------
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640 WT1 WT b1
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641 WT2 WT b2
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642 WT3 WT b3
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643 Mut1 Mut b1
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644 Mut2 Mut b2
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645 Mut3 Mut b3
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646 ========== ============ =========
0
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647
3
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648 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
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649
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650 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
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651
1
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652
0
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653 **Contrasts of Interest:**
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654 The contrasts you wish to make between levels.
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655 A common contrast would be a simple difference between two levels: "Mut-WT"
0
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656 represents the difference between the mutant and wild type genotypes.
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657 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
0
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658
3
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659 **Filter Low Counts:**
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660 Genes with very low counts across all libraries provide little evidence for differential expression.
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661 In the biological point of view, a gene must be expressed at some minimal level before
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662 it is likely to be translated into a protein or to be biologically important. In addition, the
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663 pronounced discreteness of these counts interferes with some of the statistical approximations
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664 that are used later in the pipeline. These genes should be filtered out prior to further
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665 analysis.
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666 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
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667 for any of the conditions. Users can set their own definition of genes being expressed. Usually
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668 a gene is required to have a count of 5-10 in a library to be considered expressed in that
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669 library. Users should also filter with count-per-million (CPM) rather than filtering on the
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670 counts directly, as the latter does not account for differences in library sizes between samples.
0
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671
3
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672 Option to ignore the genes that do not show significant levels of
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673 expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values:
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674
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675 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
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676 least the number of samples specified under Minimum Samples.
0
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677
3
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678 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
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679 on Total Count or Minimum Samples.
0
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680
3
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681 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
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682 with a minimum total read count.
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683
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684 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
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685 requirement must be met in order for that gene to be kept.
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diff changeset
686
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687 If the Minimum Samples filter is applied, only genes that exhibit a CPM/count greater than the required amount in at least the number of samples specified will be used for analysis. Care should be taken to
0
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688 ensure that the sample requirement is appropriate. In the case of an experiment
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689 with two experimental groups each with two members, if there is a change from
3
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690 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
0
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691 then this will cause that gene to fail the criteria. When in doubt simply do not
3
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692 filter or consult the `limma User's Guide`_ for filtering recommendations.
0
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693
3
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694 **Advanced Options:**
0
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695
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696 By default error rate for multiple testing is controlled using Benjamini and
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697 Hochberg's false discovery rate control at a threshold value of 0.05. However
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698 there are options to change this to custom values.
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699
3
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700 * **Minimum log2-fold-change Required:**
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701 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
702 multiple testing, the observation must have an absolute log2-fold-change
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703 greater than this threshold to be considered significant, thus highlighted
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diff changeset
704 in the MD plot.
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705
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706 * **Adjusted Threshold:**
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707 Set the threshold for the resulting value of the multiple testing control
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708 method. Only observations whose statistic falls below this value is
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diff changeset
709 considered significant, thus highlighted in the MD plot.
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diff changeset
710
0
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diff changeset
711 * **P-Value Adjustment Method:**
1
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712 Change the multiple testing control method, the options are BH(1995) and
0
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diff changeset
713 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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diff changeset
714 Holm(1979) which is a method for family-wise error rate control.
1
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diff changeset
715
3
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716 **Normalisation Method:**
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717 The most obvious technical factor that affects the read counts, other than gene expression
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diff changeset
718 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
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diff changeset
719 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
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diff changeset
720 part of the basic modeling procedure and flows automatically into fold-change or p-value
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diff changeset
721 calculations. It is always present, and doesn’t require any user intervention.
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diff changeset
722 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
723 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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diff changeset
724 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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diff changeset
725 This commonly becomes important when a small number of genes are very highly expressed
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diff changeset
726 in one sample, but not in another. The highly expressed genes can consume a substantial
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
727 proportion of the total library size, causing the remaining genes to be under-sampled in that
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diff changeset
728 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
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diff changeset
729 appear to be down-regulated in that sample . The edgeR `calcNormFactors` function normalizes for RNA composition by finding a set of scaling factors for the library sizes that minimize the log-fold changes between the samples for most genes. The default method for computing these scale factors uses a trimmed mean of M values (TMM) between each pair of samples. We call the product of the original library size and the scaling factor the *effective library size*. The effective library size replaces the original library size in all downsteam analyses. TMM is the recommended method for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. You can change the normalisation method under **Advanced Options** above. For more information, see the `calcNormFactors` section in the `edgeR User's Guide`_.
1
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diff changeset
730
3
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diff changeset
731 **Robust Settings**
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732 Option to use robust settings with eBayes, used by both liamm-voom and limma-trend. Using robust settings is usually recommended to protect against outlier genes, for more information see the `limma User's Guide`_. This is turned on by default.
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diff changeset
733
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734 **Prior Count:**
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735 If the limma-trend method is used, a count (`prior.count`) is added to all counts to avoid taking a log of zero, and damp down the variances of logarithms of low counts. A default of 3 is used, as recommended in the `limma User's Guide`_.
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diff changeset
736
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diff changeset
737 **Apply Sample Weights:**
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738 If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still
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diff changeset
739 used in the statistical analysis but their impact is reduced. Use this
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diff changeset
740 whenever significant outliers are present. The MDS plotting tool in this package
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diff changeset
741 is useful for identifying outliers. For more information on this option see Liu et al. (2015).
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diff changeset
742
0
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743
1
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744 **Outputs**
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745
3
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diff changeset
746 This tool outputs
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diff changeset
747
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748 * a table of differentially expressed genes for each contrast of interest
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749 * a HTML report with plots and additional information
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diff changeset
750
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751 Optionally, under **Output Options** you can choose to output
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diff changeset
752
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753 * a normalised counts table
4
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754 * the R script used by this tool
3
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diff changeset
755 * an RData file
1
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756
0
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757 -----
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758
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759 **Citations:**
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760
3
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761 Please try to cite the appropriate articles when you publish results obtained using software, as such citation is the main means by which the authors receive credit for their work.
0
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diff changeset
762
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diff changeset
763 limma
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764
1
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765 Please cite the paper below for the limma software itself. Please also try
0
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766 to cite the appropriate methodology articles that describe the statistical
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767 methods implemented in limma, depending on which limma functions you are
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768 using. The methodology articles are listed in Section 2.1 of the `limma
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769 User's Guide`_.
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770
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771 * Smyth GK (2005). Limma: linear models for microarray data. In:
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772 'Bioinformatics and Computational Biology Solutions using R and
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773 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
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774 W. Huber (eds), Springer, New York, pages 397-420.
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775
0
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776 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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777 precision weights unlock linear model analysis tools for
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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778 RNA-seq read counts. Genome Biology 15, R29.
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779
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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780 * 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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781
1
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782 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
0
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783 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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784 for microarray data. BMC Bioinformatics 7, Article 261.
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785
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786
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787 edgeR
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788
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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789 Please cite the first paper for the software itself and the other papers for
1
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790 the various original statistical methods implemented in edgeR. See
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791 Section 1.2 in the `edgeR User's Guide`_ for more detail.
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792
1
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793 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
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794 package for differential expression analysis of digital gene expression
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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795 data. Bioinformatics 26, 139-140
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796
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797 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
0
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798 differences in tag abundance. Bioinformatics 23, 2881-2887
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799
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800 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
0
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801 binomial dispersion, with applications to SAGE data.
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802 Biostatistics, 9, 321-332
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803
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804 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
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805 of multifactor RNA-Seq experiments with respect to biological variation.
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806 Nucleic Acids Research 40, 4288-4297
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807
0
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808 Please report problems or suggestions to: su.s@wehi.edu.au
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809
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810 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
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811 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
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812 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
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813 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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814 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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815 ]]></help>
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816 <citations>
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817 <citation type="doi">10.1186/gb-2014-15-2-r29</citation>
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818 <citation type="doi">10.1093/nar/gkv412</citation>
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819 </citations>
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820 </tool>