annotate limma_voom.xml @ 19:c9c6427edfe9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
author iuc
date Tue, 28 May 2019 10:04:10 -0400
parents 97e06a4c7c75
children 0921444c832d
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1 <tool id="limma_voom" name="limma" version="3.38.3+galaxy3">
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2 <description>
3
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3 Perform differential expression with limma-voom or limma-trend
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4 </description>
1
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5
0
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6 <requirements>
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7 <requirement type="package" version="3.38.3">bioconductor-limma</requirement>
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8 <requirement type="package" version="3.24.1">bioconductor-edger</requirement>
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9 <requirement type="package" version="1.4.30">r-statmod</requirement>
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10 <requirement type="package" version="1.0.0">r-scales</requirement>
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11 <requirement type="package" version="0.2.20">r-rjson</requirement>
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12 <requirement type="package" version="1.20.2">r-getopt</requirement>
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13 <requirement type="package" version="3.0.1">r-gplots</requirement>
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14 <requirement type="package" version="1.10.0">bioconductor-glimma</requirement>
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15 </requirements>
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16
1
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17 <version_command><![CDATA[
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18 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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19 ]]></version_command>
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21 <command detect_errors="exit_code"><![CDATA[
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22 #import json
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23 Rscript '$__tool_directory__/limma_voom.R'
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25 -R '$outReport'
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26 -o '$outReport.files_path'
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28 #if $input.format=="files":
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30 ## Adapted from DESeq2 wrapper
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31 #set $temp_factor_names = list()
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32 #for $fact in $input.rep_factor:
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33 #set $temp_factor = list()
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34 #for $g in $fact.rep_group:
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35 #set $count_files = list()
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36 #for $file in $g.countsFile:
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37 $count_files.append(str($file))
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38 #end for
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39 $temp_factor.append( {str($g.groupName): $count_files} )
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40 #end for
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41
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42 $temp_factor.reverse()
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43 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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44 #end for
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45 -j '#echo json.dumps(temp_factor_names)#'
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46
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47 #elif $input.format=="matrix":
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48 -m '$input.counts'
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49 #if $input.fact.ffile=='yes':
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50 -f '$input.fact.finfo'
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51 #else:
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52 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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53 #end if
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54 #end if
1
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55
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56 #if $anno.annoOpt=='yes':
3
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57 -a '$anno.geneanno'
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58 #end if
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59
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60 #if $cont.cfile=='yes':
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61 -C '$cont.cinfo'
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62 #else:
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63 -D '${ ','.join( ['%s' % $x.contrast for x in $cont.rep_contrast] ) }'
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64 #end if
1
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65
3
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66 #if $f.filt.filt_select == 'yes':
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67 #if $f.filt.cformat.format_select == 'cpm':
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68 -c '$f.filt.cformat.cpmReq'
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69 -s '$f.filt.cformat.cpmSampleReq'
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70 #elif $f.filt.cformat.format_select == 'counts':
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71 -z '$f.filt.cformat.cntReq'
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72 #if $f.filt.cformat.samples.count_select == 'total':
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73 -y
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74 #elif $f.filt.cformat.samples.count_select == 'sample':
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75 -s '$f.filt.cformat.samples.cntSampleReq'
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76 #end if
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77 #end if
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78 #end if
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79
8
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80 #if $out.plots:
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81 -P $out.plots
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82 #end if
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83
12
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84 #if $out.filtCounts:
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85 -F
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86 #end if
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87
3
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88 #if $out.normCounts:
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89 -x
1
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90 #end if
0
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91
11
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92 #if $out.libinfo:
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93 -L
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94 #end if
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95
3
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96 #if $out.rdaOption:
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97 -r
1
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98 #end if
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99
11
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100
3
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101 -l '$adv.lfc'
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102 -p '$adv.pVal'
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103 -d '$adv.pAdjust'
7
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104 -G '$adv.topgenes'
6
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105 #if $adv.treat:
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106 -T
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107 #end if
0
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108
3
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109 #if $deMethod.de_select == 'voom':
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110 #if $deMethod.weightOption:
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111 -w
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112 #end if
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113 #elif $deMethod.de_select == 'trend':
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114 -t $deMethod.prior_count
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115 #end if
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116
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117 -n '$adv.normalisationOption'
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118
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119 #if $adv.robOption:
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120 -b
1
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121 #end if
0
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122
1
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123 &&
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124 mkdir ./output_dir
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125
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126 &&
14
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127 cp '$outReport.files_path'/*tsv output_dir/
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128
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129 #if 'i' in str($out.plots).split( "," ):
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130 && cp -r ./glimma* '$outReport.files_path'
9
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131 #end if
13
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132
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133 #if $out.filtCounts or $out.normCounts:
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134 && cp '$outReport.files_path'/*counts output_dir/
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135 #end if
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136
4
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137 #if $out.rscript:
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138 && cp '$__tool_directory__/limma_voom.R' '$rscript'
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139 #end if
1
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140 ]]></command>
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141
0
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142 <inputs>
3
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143
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144 <!-- DE Method Option -->
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145 <conditional name="deMethod">
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146 <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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147 <option value="voom" selected="True">limma-voom</option>
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148 <option value="trend">limma-trend</option>
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149 </param>
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150 <when value="voom">
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151 <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality weights?"
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152 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False.">
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153 </param>
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154 </when>
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155 <when value="trend">
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156 <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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157 </when>
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158 </conditional>
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159 <!-- Counts and Factors -->
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160 <conditional name="input">
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161 <param name="format" type="select" label="Count Files or Matrix?"
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162 help="You can choose to input either separate count files (one per sample) or a single count matrix">
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163 <option value="files">Separate Count Files</option>
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164 <option value="matrix">Single Count Matrix</option>
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165 </param>
1
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166
3
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167 <when value="files">
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168 <repeat name="rep_factor" title="Factor" min="1">
17
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169 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
3
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170 <sanitizer>
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171 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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172 </sanitizer>
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173 </param>
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174 <repeat name="rep_group" title="Group" min="2" default="2">
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175 <param name="groupName" type="text" label="Name"
17
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176 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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177 <sanitizer>
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178 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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179 </sanitizer>
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180 </param>
4
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181 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
3
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182 </repeat>
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183 </repeat>
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184 </when>
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185
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186 <when value="matrix">
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187 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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188
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189 <conditional name="fact">
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190 <param name="ffile" type="select" label="Input factor information from file?"
17
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191 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
3
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192 <option value="no">No</option>
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193 <option value="yes">Yes</option>
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194 </param>
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195 <when value="yes">
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196 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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197 </when>
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198 <when value="no" >
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199 <repeat name="rep_factor" title="Factor" min="1">
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200 <param name="factorName" type="text" label="Factor Name"
17
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201 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
3
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202 <validator type="empty_field" />
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203 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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204 </param>
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205 <param name="groupNames" type="text" label="Groups"
17
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206 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens.">
3
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207 <validator type="empty_field" />
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208 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
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209 </param>
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210 </repeat>
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211 </when>
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212 </conditional>
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213 </when>
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214 </conditional>
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215
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216 <!-- Gene Annotations -->
0
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217 <conditional name="anno">
1
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218 <param name="annoOpt" type="select" label="Use Gene Annotations?"
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219 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene, and used to label the top genes in the Volcano plot. Interactive Glimma Volcano and MD plots will also be generated. See Help section below.">
0
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220 <option value="no">No</option>
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221 <option value="yes">Yes</option>
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222 </param>
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223 <when value="yes">
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224 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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225 </when>
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226 <when value="no" />
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227 </conditional>
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228
3
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229 <!-- Contrasts -->
19
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230 <conditional name="cont">
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231 <param name="cfile" type="select" label="Input Contrast information from file?"
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232 help="You can choose to input the contrast information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens. Use a hyphen to separate the groups you want to compare, as shown in the Help section below.">
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233 <option value="no">No</option>
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234 <option value="yes">Yes</option>
0
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235 </param>
19
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236 <when value="yes">
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237 <param name="cinfo" type="data" format="tabular" label="Contrasts File"/>
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238 </when>
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239 <when value="no" >
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240 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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241 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
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242 <validator type="empty_field" />
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243 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
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244 </param>
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245 </repeat>
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246 </when>
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247 </conditional>
1
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248
3
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249 <!-- Filter Options -->
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250 <section name="f" expanded="false" title="Filter Low Counts">
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251 <conditional name="filt">
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252 <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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253 <option value="no" selected="true">No</option>
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254 <option value="yes">Yes</option>
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255 </param>
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256 <when value="yes">
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257 <conditional name="cformat">
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258 <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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259 <option value="cpm">CPM</option>
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260 <option value="counts">Counts</option>
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261 </param>
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262 <when value="cpm">
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263 <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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264 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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265 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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266 </when>
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267 <when value="counts">
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268 <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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269 <conditional name="samples">
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270 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
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271 <option value="total">Total</option>
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272 <option value="sample">Sample</option>
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273 </param>
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274 <when value="total">
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275 <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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276 </when>
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277 <when value="sample">
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278 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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279 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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280 </when>
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281 </conditional>
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282 </when>
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283 </conditional>
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284 </when>
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285 <when value="no" />
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286 </conditional>
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287 </section>
1
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288
3
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289 <!-- Output Options -->
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290 <section name="out" expanded="false" title="Output Options">
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291 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report">
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292 <option value="i" selected="True">Glimma Interactive Plots</option>
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293 <option value="d">Density Plots (if filtering)</option>
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294 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
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295 <option value="b">Box Plots (if normalising)</option>
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296 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
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297 <option value="m">MD Plots for individual samples</option>
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298 <option value="h">Heatmaps (top DE genes) </option>
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299 <option value="s">Stripcharts (top DE genes)</option>
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300 </param>
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301 <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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302 label="Output Filtered Counts Table?"
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303 help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
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304 </param>
3
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305 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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306 label="Output Normalised Counts Table?"
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307 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
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308 </param>
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309 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
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310 label="Output Library information file?"
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311 help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No">
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312 </param>
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313 <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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314 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
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315 label="Output RData file?"
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316 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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317 </param>
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318 </section>
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319
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320 <!-- Advanced Options -->
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321 <section name="adv" expanded="false" title="Advanced Options">
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322 <param name="lfc" type="float" value="0" min="0"
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323 label="Minimum Log2 Fold Change"
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324 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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325 <param name="pVal" type="float" value="0.05" min="0" max="1"
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326 label="P-Value Adjusted Threshold"
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327 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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328 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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329 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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330 <option value="BY">Benjamini and Yekutieli (2001)</option>
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331 <option value="holm">Holm (1979)</option>
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332 <option value="none">None</option>
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333 </param>
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334 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
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335 label="Test significance relative to a fold-change threshold (TREAT)"
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336 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
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337 <param name="topgenes" type="integer" value="10" min="0" max="100"
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338 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
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339 help="The top DE genes will be highlighted in the Volcano plot for each contrast and can be output in heatmap and stripchart PDFs (max 100). Default: 10."/>
3
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340 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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341 <option value="TMM" selected="true">TMM</option>
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342 <option value="RLE">RLE</option>
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343 <option value="upperquartile">Upperquartile</option>
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344 <option value="none">None (Don't normalise)</option>
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345 </param>
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346 <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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347 </section>
0
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348
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349 </inputs>
1
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350
0
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351 <outputs>
1
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352 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
13
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353 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables">
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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354 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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355 </collection>
13
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356 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts">
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357 <filter>out['filtCounts']</filter>
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358 </data>
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359 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts">
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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360 <filter>out['normCounts']</filter>
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361 </data>
4
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362 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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363 <filter>out['rscript']</filter>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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364 </data>
11
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365 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
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366 <filter>out['libinfo']</filter>
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367 </data>
0
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368 </outputs>
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369
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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370 <tests>
3
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371 <!-- Ensure report is output -->
17
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372 <test expect_num_outputs="2">
3
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373 <param name="format" value="matrix" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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374 <param name="counts" value="matrix.txt" />
3
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375 <repeat name="rep_factor">
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376 <param name="factorName" value="Genotype"/>
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377 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
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378 </repeat>
19
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379 <param name="cfile" value="no" />
3
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iuc
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380 <repeat name="rep_contrast">
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381 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
382 </repeat>
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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383 <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
384 <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
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385 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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386 <param name="normalisationOption" value="TMM" />
7
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387 <param name="topgenes" value="6" />
1
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388 <output_collection name="outTables" count="2">
4
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389 <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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390 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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391 <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
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392 <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
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393 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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diff changeset
394 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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diff changeset
395 <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
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396 <assert_contents>
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diff changeset
397 <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
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398 <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
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399 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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400 </element>
1
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401 </output_collection>
0
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402 <output name="outReport" >
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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403 <assert_contents>
3
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404 <has_text text="Limma Analysis Output" />
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405 <has_text text="Glimma Interactive Results" />
0
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406 <not_has_text text="RData" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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407 </assert_contents>
1
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408 </output>
4
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409 </test>
3
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410 <!-- Ensure annotation file input works -->
17
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411 <test expect_num_outputs="2">
3
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412 <param name="format" value="matrix" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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413 <param name="annoOpt" value="yes" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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414 <param name="geneanno" value="anno.txt" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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415 <param name="counts" value="matrix.txt" />
3
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diff changeset
416 <repeat name="rep_factor">
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iuc
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diff changeset
417 <param name="factorName" value="Genotype"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
418 <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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419 </repeat>
19
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parents: 18
diff changeset
420 <param name="cfile" value="no" />
3
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parents: 2
diff changeset
421 <repeat name="rep_contrast">
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iuc
parents: 2
diff changeset
422 <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
423 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
424 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
425 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
426 <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
427 <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
428 <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
429 <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
430 <has_text_matching expression="11304.*Abca4.*0.4573" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
431 </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
432 </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
433 </output_collection>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
434 </test>
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
435 <!-- Ensure Rscript and RData file can be output -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
436 <test expect_num_outputs="3">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
437 <param name="format" value="matrix" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
438 <param name="rscript" value="True"/>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
439 <param name="rdaOption" value="true" />
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
440 <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
441 <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
442 <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
443 <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
444 </repeat>
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
445 <param name="cfile" value="no" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
446 <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
447 <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
448 </repeat>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
449 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
450 <param name="topgenes" value="6" />
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
451 <output name="outReport" >
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
452 <assert_contents>
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
453 <has_text text="RData" />
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
454 </assert_contents>
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
455 </output>
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
456 <output name="rscript">
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
457 <assert_contents>
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
458 <has_text_matching expression="Task run time" />
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
459 </assert_contents>
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
460 </output>
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
461 </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
462 <!-- Ensure secondary factors work -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
463 <test expect_num_outputs="2">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
464 <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
465 <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
466 <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
467 <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
468 <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
469 </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
470 <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
471 <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
472 <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
473 </repeat>
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
474 <param name="cfile" value="no" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
475 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
476 <param name="contrast" value="Mut-WT" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
477 </repeat>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
478 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
479 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
480 <output_collection name="outTables" count="1" >
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
481 <element name="limma-voom_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
482 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
483 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
484 <has_text_matching expression="11304.*0.4590" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
485 </assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
486 </element>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
487 </output_collection>
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
488 </test>
14
3133e833b3ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents: 13
diff changeset
489 <!-- Ensure factors file with unordered samples works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
490 <test expect_num_outputs="2">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
491 <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
492 <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
493 <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
494 <param name="counts" value="matrix.txt" />
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
495 <param name="cfile" value="no" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
496 <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
497 <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
498 </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
499 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
500 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
501 <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
502 <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
503 <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
504 <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
505 <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
506 </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
507 </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
508 </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
509 </test>
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
510 <!-- Ensure filtered and normalised count outputs works-->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
511 <test expect_num_outputs="4">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
512 <param name="format" value="matrix" />
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
513 <param name="filtCounts" value="true" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
514 <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
515 <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
516 <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
517 <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
518 <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
519 </repeat>
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
520 <param name="cfile" value="no" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
521 <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
522 <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
523 </repeat>
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
524 <param name="filt_select" value="yes" />
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
525 <param name="format_select" value="counts"/>
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
526 <param name="cntReq" value="10"/>
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
527 <param name="count_select" value="sample"/>
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
528 <param name="cntSampleReq" value="3"/>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
529 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
530 <param name="topgenes" value="6" />
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
531 <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
532 <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
533 <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
534 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
535 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
536 </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
537 </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
538 </output_collection>
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
539 <output name="outNorm" ftype="tabular" >
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
540 <assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
541 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
542 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
543 </assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
544 </output>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
545 <output name="outFilt" ftype="tabular" >
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
546 <assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
547 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
548 <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
549 <not_has_text text="11302"/>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
550 </assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
551 </output>
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
552 </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
553 <!-- Ensure multiple counts files input works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
554 <test expect_num_outputs="3">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
555 <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
556 <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
557 <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
558 <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
559 <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
560 <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
561 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
562 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
563 <param name="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
564 <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
565 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
566 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
567 <repeat 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
568 <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
569 <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
570 <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
571 <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
572 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
573 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
574 <param name="groupName" value="b2"/>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
575 <param name="countsFile" value="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
576 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
577 <repeat name="rep_group">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
578 <param name="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
579 <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
580 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
581 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
582 <param name="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
583 <param name="geneanno" value="anno.txt" />
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
584 <param name="cfile" value="no" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
585 <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
586 <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
587 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
588 <repeat name="rep_contrast">
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
589 <param name="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
590 </repeat>
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
591 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
592 <param name="normCounts" value="true" />
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
593 <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
594 <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
595 <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
596 <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
597 <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
598 </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
599 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
600 <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
601 <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
602 <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
603 <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
604 </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
605 </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
606 </output_collection>
13
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
607 <output name="outNorm" ftype="tabular" >
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
608 <assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
609 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
610 <has_text_matching expression="11304.*Abca4.*15.7545" />
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
611 </assert_contents>
d5a940112511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents: 12
diff changeset
612 </output>
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
613 </test>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
614 <!-- Ensure limma-trend option works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
615 <test expect_num_outputs="2">
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
616 <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
617 <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
618 <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
619 <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
620 <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
621 </repeat>
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
622 <param name="cfile" value="no" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
623 <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
624 <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
625 </repeat>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
626 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
627 <param name="topgenes" value="6" />
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
628 <param name="de_select" value="trend" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
629 <output name="outReport" >
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
630 <assert_contents>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
631 <has_text text="The limma-trend method was used" />
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
632 </assert_contents>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
633 </output>
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
634 <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
635 <element name="limma-trend_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
636 <assert_contents>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
637 <has_text_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
638 <has_text_matching expression="11304.*0.4540" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
639 </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
640 </element>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
641 </output_collection>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
642 </test>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
643 <!-- Ensure limma-trend option with annotation works -->
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
644 <test expect_num_outputs="2">
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
645 <param name="format" value="matrix" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
646 <param name="counts" value="matrix.txt" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
647 <param name="annoOpt" value="yes" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
648 <param name="geneanno" value="anno.txt" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
649 <repeat name="rep_factor">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
650 <param name="factorName" value="Genotype"/>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
651 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
652 </repeat>
19
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
653 <param name="cfile" value="no" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
654 <repeat name="rep_contrast">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
655 <param name="contrast" value="Mut-WT" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
656 </repeat>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
657 <param name="normalisationOption" value="TMM" />
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
658 <param name="topgenes" value="6" />
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
659 <param name="de_select" value="trend" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
660 <output name="outReport" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
661 <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
662 <has_text text="The limma-trend method was used" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
663 </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
664 </output>
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
665 <output_collection name="outTables" count="1">
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
666 <element name="limma-trend_Mut-WT" ftype="tabular" >
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
667 <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
668 <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
669 <has_text_matching expression="11304.*0.4540" />
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
670 </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
671 </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
672 </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
673 </test>
17
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
674 <!-- Ensure samples and groups beginning with numbers can be handled -->
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
675 <test expect_num_outputs="3">
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
676 <param name="format" value="matrix" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
677 <param name="counts" value="matrix_num.txt" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
678 <param name="annoOpt" value="yes" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
679 <param name="geneanno" value="anno.txt" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents: 16
diff changeset
680 <repeat name="rep_factor">
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681 <param name="factorName" value="Group"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
682 <param name="groupNames" value="2,2,2,1,1,1" />
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683 </repeat>
19
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684 <param name="cfile" value="no" />
17
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diff changeset
685 <repeat name="rep_contrast">
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diff changeset
686 <param name="contrast" value="2-1" />
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687 </repeat>
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diff changeset
688 <param name="filt_select" value="yes" />
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diff changeset
689 <param name="format_select" value="counts"/>
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iuc
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690 <param name="cntReq" value="10"/>
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diff changeset
691 <param name="count_select" value="sample"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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692 <param name="cntSampleReq" value="3"/>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
693 <param name="normalisationOption" value="TMM" />
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diff changeset
694 <param name="normCounts" value="true" />
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diff changeset
695 <param name="topgenes" value="6" />
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diff changeset
696 <param name="de_select" value="voom" />
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diff changeset
697 <output_collection name="outTables" count="1">
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diff changeset
698 <element name="limma-voom_X2-X1" ftype="tabular" >
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diff changeset
699 <assert_contents>
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diff changeset
700 <has_text_matching expression="EntrezID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
701 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
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702 </assert_contents>
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diff changeset
703 </element>
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diff changeset
704 </output_collection>
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diff changeset
705 <output name="outNorm" ftype="tabular" >
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
706 <assert_contents>
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diff changeset
707 <has_text_matching expression="EntrezID.*2-1.*2-2.*2-3.*1-1.*1-2.*1-3" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
708 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
709 </assert_contents>
86b3df7db58b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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diff changeset
710 </output>
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diff changeset
711 </test>
19
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diff changeset
712 <!-- Ensure contrasts file works -->
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diff changeset
713 <test expect_num_outputs="2">
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
714 <param name="format" value="matrix" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
715 <param name="counts" value="matrix.txt" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
716 <repeat name="rep_factor">
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
717 <param name="factorName" value="Genotype"/>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
718 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
719 </repeat>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
720 <param name="cfile" value="yes" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
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diff changeset
721 <param name="cinfo" value="contrasts.txt" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
722 <param name="normalisationOption" value="TMM" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
723 <param name="topgenes" value="6" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
diff changeset
724 <output_collection name="outTables" count="2">
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
725 <element name="limma-voom_Mut-WT" ftype="tabular" >
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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726 <assert_contents>
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parents: 18
diff changeset
727 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
728 <has_text_matching expression="11304.*0.4573" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
729 </assert_contents>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
730 </element>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
731 <element name="limma-voom_WT-Mut" ftype="tabular" >
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
732 <assert_contents>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
733 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
734 <has_text_matching expression="11304.*-0.4573" />
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
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735 </assert_contents>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
736 </element>
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
diff changeset
737 </output_collection>
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diff changeset
738 </test>
0
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diff changeset
739 </tests>
1
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parents: 0
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740
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diff changeset
741 <help><![CDATA[
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
742 .. class:: infomark
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743
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
744 **What it does**
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745
14
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diff changeset
746 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. Interactive Glimma_ plots and tables can also be generated and links to the Glimma plots will be provided in the report. See an example workflow here_.
3
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diff changeset
747
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748 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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diff changeset
749
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750 -----
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
751
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diff changeset
752 **Inputs**
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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753
3
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diff changeset
754 **Differential Expression Method:**
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diff changeset
755 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom.
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diff changeset
756 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most
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diff changeset
757 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
758 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
759
0
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diff changeset
760 **Counts Data:**
16
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761 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
3
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parents: 2
diff changeset
762
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diff changeset
763 Example - **Separate Count Files**:
0
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764
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
765 ========== =======
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
766 **GeneID** **WT1**
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
767 ---------- -------
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
768 11287 1699
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
769 11298 1905
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
770 11302 6
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
771 11303 2099
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
772 11304 356
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
773 11305 2528
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
774 ========== =======
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
775
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
776 Example - **Single Count Matrix**:
0
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iuc
parents:
diff changeset
777
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
778 ========== ======= ======= ======= ======== ======== ========
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
779 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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780 ---------- ------- ------- ------- -------- -------- --------
1
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iuc
parents: 0
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781 11287 1699 1528 1601 1463 1441 1495
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iuc
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782 11298 1905 1744 1834 1345 1291 1346
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iuc
parents: 0
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783 11302 6 8 7 5 6 5
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
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784 11303 2099 1974 2100 1574 1519 1654
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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785 11304 356 312 337 361 397 346
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
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786 11305 2528 2438 2493 1762 1942 2027
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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787 ========== ======= ======= ======= ======== ======== ========
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
788
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
789 **Gene Annotations:**
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
790 Optional input for gene annotations, this can contain more
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
791 information about the genes than just an ID number. The annotations will
14
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parents: 13
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792 be available in the differential expression results table and the optional normalised counts table. They will also be used to generate interactive Glimma_ Volcano, MD plots and tables of differential expression. The input annotation file must contain a header row and have the gene IDs in the first column. The second column will be used to label the genes in the Volcano plot and interactive Glimma plots, additional columns will be available in the Glimma interactive table. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
0
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diff changeset
793
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
794 Example:
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
795
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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796 ========== ========== ===================================================
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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797 **GeneID** **Symbol** **GeneName**
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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798 ---------- ---------- ---------------------------------------------------
4
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parents: 3
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799 11287 Pzp pregnancy zone protein
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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800 11298 Aanat arylalkylamine N-acetyltransferase
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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801 11302 Aatk apoptosis-associated tyrosine kinase
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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802 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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803 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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iuc
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804 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0
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805 ========== ========== ===================================================
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806
1
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iuc
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807 **Factor Information:**
14
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808 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
1
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iuc
parents: 0
diff changeset
809
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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diff changeset
810 Example:
0
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diff changeset
811
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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812 ========== ============ =========
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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diff changeset
813 **Sample** **Genotype** **Batch**
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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814 ---------- ------------ ---------
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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diff changeset
815 WT1 WT b1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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816 WT2 WT b2
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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817 WT3 WT b3
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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818 Mut1 Mut b1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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diff changeset
819 Mut2 Mut b2
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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diff changeset
820 Mut3 Mut b3
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821 ========== ============ =========
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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822
17
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diff changeset
823 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
3
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parents: 2
diff changeset
824
17
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diff changeset
825 *Groups:* The names of the groups for the factor. The names should only contain letters, numbers and underscores, other characters such as spaces and hyphens MUST not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. If the group names begin with a number an X will be added as a prefix.
1
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diff changeset
826
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
827 **Contrasts of Interest:**
19
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diff changeset
828 The contrasts you wish to make between levels. A common contrast would be a simple difference between two levels: "Mut-WT"
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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diff changeset
829 represents the difference between the mutant and wild type genotypes. Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. Alternatively, a tab-separated file can be input that has the names of the comparisons in the first column and one header row, as shown below.
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
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830
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831 Example:
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
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832
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
diff changeset
833 ============= =
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
diff changeset
834 **Contrasts**
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
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835 ------------- -
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
836 Mut-WT
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents: 18
diff changeset
837 WT-Mut
c9c6427edfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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parents: 18
diff changeset
838 ============= =
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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839
3
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parents: 2
diff changeset
840 **Filter Low Counts:**
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diff changeset
841 Genes with very low counts across all libraries provide little evidence for differential expression.
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diff changeset
842 In the biological point of view, a gene must be expressed at some minimal level before
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
843 it is likely to be translated into a protein or to be biologically important. In addition, the
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
844 pronounced discreteness of these counts interferes with some of the statistical approximations
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
845 that are used later in the pipeline. These genes should be filtered out prior to further
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
846 analysis.
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diff changeset
847 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
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diff changeset
848 for any of the conditions. Users can set their own definition of genes being expressed. Usually
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
849 a gene is required to have a count of 5-10 in a library to be considered expressed in that
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850 library. Users should also filter with count-per-million (CPM) rather than filtering on the
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diff changeset
851 counts directly, as the latter does not account for differences in library sizes between samples.
0
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852
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853 Option to ignore the genes that do not show significant levels of
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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854 expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values:
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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855
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856 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
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857 least the number of samples specified under Minimum Samples.
0
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diff changeset
858
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859 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
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860 on Total Count or Minimum Samples.
0
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861
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862 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
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diff changeset
863 with a minimum total read count.
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diff changeset
864
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865 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
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866 requirement must be met in order for that gene to be kept.
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diff changeset
867
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868 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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869 ensure that the sample requirement is appropriate. In the case of an experiment
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870 with two experimental groups each with two members, if there is a change from
3
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871 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
0
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872 then this will cause that gene to fail the criteria. When in doubt simply do not
3
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873 filter or consult the `limma User's Guide`_ for filtering recommendations.
0
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874
3
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875 **Advanced Options:**
0
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876
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877 By default error rate for multiple testing is controlled using Benjamini and
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878 Hochberg's false discovery rate control at a threshold value of 0.05. However
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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879 there are options to change this to custom values.
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880
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881 * **Minimum log2-fold-change Required:**
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882 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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883 multiple testing, the observation must have an absolute log2-fold-change
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884 greater than this threshold to be considered significant, thus highlighted
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885 in the MD plot.
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886
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887 * **Adjusted Threshold:**
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888 Set the threshold for the resulting value of the multiple testing control
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889 method. Only observations whose statistic falls below this value is
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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890 considered significant, thus highlighted in the MD plot.
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891
0
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892 * **P-Value Adjustment Method:**
1
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893 Change the multiple testing control method, the options are BH(1995) and
0
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894 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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895 Holm(1979) which is a method for family-wise error rate control.
1
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896
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897 **Testing relative to a threshold (TREAT):**
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898 If there are a lot of differentially expressed genes, a fold change threshold can be applied in addition to the P-value threshold to select genes that are more likely to be biologically significant. However, ranking by P-value and discarding genes with small logFCs can increase the false discovery rate. Using the limma TREAT function performs this analysis correctly (`McCarthy and Smyth, 2009`_).
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899
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900 **Normalisation Method:**
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901 The most obvious technical factor that affects the read counts, other than gene expression
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902 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
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903 analysis for varying sequencing depths as represented by differing library sizes. This is
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904 part of the basic modeling procedure and flows automatically into fold-change or p-value
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905 calculations. It is always present, and doesn’t require any user intervention.
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906 The second most important technical influence on differential expression is one that is less
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907 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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908 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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909 This commonly becomes important when a small number of genes are very highly expressed
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910 in one sample, but not in another. The highly expressed genes can consume a substantial
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911 proportion of the total library size, causing the remaining genes to be under-sampled in that
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912 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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913 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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914
3
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915 **Robust Settings**
6
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916 Option to use robust settings with eBayes or TREAT, used by both limma-voom and limma-trend. Using robust settings is usually recommended to protect against outlier genes, for more information see the `limma User's Guide`_ and `Phipson et al. 2016`_. This is turned on by default.
3
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917
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918 **Prior Count:**
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919 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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920
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921 **Apply Sample Weights:**
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922 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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923 used in the statistical analysis but their impact is reduced. Use this
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924 whenever significant outliers are present. The MDS plotting tool in this package
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diff changeset
925 is useful for identifying outliers. For more information on this option see Liu et al. (2015).
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926
0
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927
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928 **Outputs**
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929
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930 This tool outputs
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931
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diff changeset
932 * a table of differentially expressed genes for each contrast of interest
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diff changeset
933 * a HTML report with plots and additional information
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parents: 2
diff changeset
934
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parents: 2
diff changeset
935 Optionally, under **Output Options** you can choose to output
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parents: 2
diff changeset
936
14
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diff changeset
937 * interactive Glimma plots and tables: MDS plot, and (if annotation file is input) Volcano plot and MD plot (default: Yes)
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parents: 13
diff changeset
938 * additional plots in the report and as PDFs
3
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parents: 2
diff changeset
939 * a normalised counts table
11
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parents: 10
diff changeset
940 * a library size information file
4
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parents: 3
diff changeset
941 * the R script used by this tool
3
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parents: 2
diff changeset
942 * an RData file
1
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diff changeset
943
0
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diff changeset
944 -----
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
945
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parents:
diff changeset
946 **Citations:**
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diff changeset
947
3
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diff changeset
948 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
949
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diff changeset
950 limma
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diff changeset
951
1
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diff changeset
952 Please cite the paper below for the limma software itself. Please also try
0
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diff changeset
953 to cite the appropriate methodology articles that describe the statistical
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diff changeset
954 methods implemented in limma, depending on which limma functions you are
3
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diff changeset
955 using. The methodology articles are listed in Section 2.1 of the `limma
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diff changeset
956 User's Guide`_.
0
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diff changeset
957
1
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diff changeset
958 * Smyth GK (2005). Limma: linear models for microarray data. In:
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diff changeset
959 'Bioinformatics and Computational Biology Solutions using R and
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diff changeset
960 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
0
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diff changeset
961 W. Huber (eds), Springer, New York, pages 397-420.
1
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diff changeset
962
0
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diff changeset
963 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:
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iuc
parents:
diff changeset
964 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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parents:
diff changeset
965 RNA-seq read counts. Genome Biology 15, R29.
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diff changeset
966
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diff changeset
967 * Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.
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diff changeset
968
1
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diff changeset
969 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
0
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diff changeset
970 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
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diff changeset
971 for microarray data. BMC Bioinformatics 7, Article 261.
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diff changeset
972
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diff changeset
973
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diff changeset
974 edgeR
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diff changeset
975
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diff changeset
976 Please cite the first paper for the software itself and the other papers for
1
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parents: 0
diff changeset
977 the various original statistical methods implemented in edgeR. See
3
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diff changeset
978 Section 1.2 in the `edgeR User's Guide`_ for more detail.
0
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diff changeset
979
1
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parents: 0
diff changeset
980 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
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parents: 0
diff changeset
981 package for differential expression analysis of digital gene expression
0
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diff changeset
982 data. Bioinformatics 26, 139-140
1
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parents: 0
diff changeset
983
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parents: 0
diff changeset
984 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
0
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diff changeset
985 differences in tag abundance. Bioinformatics 23, 2881-2887
1
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parents: 0
diff changeset
986
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diff changeset
987 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
0
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diff changeset
988 binomial dispersion, with applications to SAGE data.
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
989 Biostatistics, 9, 321-332
1
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990
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diff changeset
991 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
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diff changeset
992 of multifactor RNA-Seq experiments with respect to biological variation.
0
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993 Nucleic Acids Research 40, 4288-4297
1
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994
0
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diff changeset
995 Please report problems or suggestions to: su.s@wehi.edu.au
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996
3
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diff changeset
997 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
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diff changeset
998 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html
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diff changeset
999 .. _here: https://f1000research.com/articles/5-1408/v3
3
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1000 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
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diff changeset
1001 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
0
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1002 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
3
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1003 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
6
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diff changeset
1004 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553
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1005 .. _Phipson et al. 2016: https://www.ncbi.nlm.nih.gov/pubmed/28367255
1
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1006 ]]></help>
0
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1007 <citations>
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1008 <citation type="doi">10.1186/gb-2014-15-2-r29</citation>
0
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1009 <citation type="doi">10.1093/nar/gkv412</citation>
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1010 </citations>
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1011 </tool>