annotate edger.xml @ 2:a1634a9c2ee1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
author iuc
date Thu, 19 Apr 2018 17:26:38 -0400
parents 2a16413ec60d
children d79ed3ec25fe
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a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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1 <tool id="edger" name="edgeR" version="3.20.7.1">
0
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2 <description>
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3 Perform differential expression of count data
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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4 </description>
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6 <requirements>
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7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
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8 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
0
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9 <requirement type="package" version="0.2.15">r-rjson</requirement>
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10 <requirement type="package" version="1.20.0">r-getopt</requirement>
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11 <requirement type="package" version="1.4.30">r-statmod</requirement>
0
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12 <!-- required for alpha function used with plotMD -->
1
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13 <requirement type="package" version="0.5.0">r-scales</requirement>
0
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14 </requirements>
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9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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16 <version_command><![CDATA[
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17 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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18 ]]></version_command>
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20 <command detect_errors="exit_code"><![CDATA[
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21 #import json
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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22 Rscript '$__tool_directory__/edger.R'
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23
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24 -R '$outReport'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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25 -o '$outReport.files_path'
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26
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27 #if $input.format=="files":
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29 ## Adapted from DESeq2 wrapper
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30 #set $temp_factor_names = list()
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31 #for $fact in $input.rep_factor:
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32 #set $temp_factor = list()
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33 #for $g in $fact.rep_group:
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34 #set $count_files = list()
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35 #for $file in $g.countsFile:
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36 $count_files.append(str($file))
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37 #end for
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38 $temp_factor.append( {str($g.groupName): $count_files} )
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39 #end for
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40
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41 $temp_factor.reverse()
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42 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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43 #end for
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44 -j '#echo json.dumps(temp_factor_names)#'
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45
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46 #elif $input.format=="matrix":
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47 -m '$input.counts'
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48 #if $input.fact.ffile=='yes':
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49 -f '$input.fact.finfo'
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50 #else:
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51 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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52 #end if
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53 #end if
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54
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55 #if $anno.annoOpt=='yes':
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56 -a '$anno.geneanno'
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57 #end if
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58
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59 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
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60
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61 #if $f.filt.filt_select == 'yes':
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62 #if $f.filt.cformat.format_select == 'cpm':
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63 -c '$f.filt.cformat.cpmReq'
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64 -s '$f.filt.cformat.cpmSampleReq'
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65 #elif $f.filt.cformat.format_select == 'counts':
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66 -z '$f.filt.cformat.cntReq'
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67 #if $f.filt.cformat.samples.count_select == 'total':
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68 -y
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69 #elif $f.filt.cformat.samples.count_select == 'sample':
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70 -s '$f.filt.cformat.samples.cntSampleReq'
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71 #end if
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72 #end if
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73 #end if
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74
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75 #if $out.normCounts:
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76 -x
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77 #end if
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78 #if $out.rdaOption:
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79 -r
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80 #end if
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81
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82 -l '$adv.lfc'
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83 -p '$adv.pVal'
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84 -d '$adv.pAdjust'
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85 -n '$adv.normalisationOption'
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86 #if $adv.robOption:
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87 -b
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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88 #end if
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89 #if $adv.lrtOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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90 -t
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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91 #end if
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92
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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93 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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94 mkdir ./output_dir
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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95
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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96 &&
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97 cp '$outReport.files_path'/*.tsv output_dir/
2
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98
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99 #if $out.rscript:
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100 && cp '$__tool_directory__/edger.R' '$rscript'
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101 #end if
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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102 ]]></command>
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103
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104 <inputs>
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105
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106 <!-- Counts and Factors -->
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107 <conditional name="input">
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108 <param name="format" type="select" label="Count Files or Matrix?"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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109 help="You can choose to input either separate count files (one per sample) or a single count matrix">
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110 <option value="files">Separate Count Files</option>
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111 <option value="matrix">Single Count Matrix</option>
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112 </param>
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113
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114 <when value="files">
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115 <repeat name="rep_factor" title="Factor" min="1">
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116 <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.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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117 <sanitizer>
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118 <valid initial="string.letters,string.digits"><add value="_" /></valid>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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119 </sanitizer>
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120 </param>
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121 <repeat name="rep_group" title="Group" min="2" default="2">
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122 <param name="groupName" type="text" label="Name"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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123 help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
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124 <sanitizer>
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125 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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126 </sanitizer>
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127 </param>
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128 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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129 </repeat>
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130 </repeat>
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131 </when>
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132
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133 <when value="matrix">
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134 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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135
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136 <conditional name="fact">
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137 <param name="ffile" type="select" label="Input factor information from file?"
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138 help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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139 <option value="no">No</option>
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140 <option value="yes">Yes</option>
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141 </param>
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142 <when value="yes">
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143 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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144 </when>
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145 <when value="no" >
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146 <repeat name="rep_factor" title="Factor" min="1">
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147 <param name="factorName" type="text" label="Factor Name"
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148 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.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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149 <validator type="empty_field" />
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150 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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151 </param>
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152 <param name="groupNames" type="text" label="Groups"
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153 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).">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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154 <validator type="empty_field" />
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155 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
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156 </param>
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157 </repeat>
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158 </when>
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159 </conditional>
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160 </when>
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161 </conditional>
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162
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163 <!-- Gene Annotations -->
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164 <conditional name="anno">
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165 <param name="annoOpt" type="select" label="Use Gene Annotations?"
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166 help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene. See Help section below.">
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167 <option value="no">No</option>
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168 <option value="yes">Yes</option>
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169 </param>
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170 <when value="yes">
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171 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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172 </when>
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173 <when value="no" />
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174 </conditional>
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175
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176 <!-- Contrasts -->
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177 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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178 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
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179 <validator type="empty_field" />
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180 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
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181 </param>
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182 </repeat>
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183
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184 <!-- Filter Options -->
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185 <section name="f" expanded="false" title="Filter Low Counts">
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186 <conditional name="filt">
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187 <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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188 <option value="no" selected="true">No</option>
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189 <option value="yes">Yes</option>
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190 </param>
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191 <when value="yes">
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192 <conditional name="cformat">
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193 <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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194 <option value="cpm">CPM</option>
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195 <option value="counts">Counts</option>
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196 </param>
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197 <when value="cpm">
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198 <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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199 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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200 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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201 </when>
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202 <when value="counts">
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203 <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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204 <conditional name="samples">
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205 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
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206 <option value="total">Total</option>
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207 <option value="sample">Sample</option>
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208 </param>
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209 <when value="total">
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210 <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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211 </when>
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212 <when value="sample">
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213 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
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214 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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215 </when>
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216 </conditional>
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217 </when>
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218 </conditional>
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219 </when>
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220 <when value="no" />
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221 </conditional>
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222 </section>
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223
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224 <!-- Output Options -->
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225 <section name="out" expanded="false" title="Output Options">
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226 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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227 label="Output Normalised Counts Table?"
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228 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
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229 </param>
2
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230 <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"/>
0
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231 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
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232 label="Output RData file?"
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233 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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234 </param>
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235 </section>
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236
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237 <!-- Advanced Options -->
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238 <section name="adv" expanded="false" title="Advanced Options">
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239 <param name="lfc" type="float" value="0" min="0"
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240 label="Minimum Log2 Fold Change"
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241 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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242 <param name="pVal" type="float" value="0.05" min="0" max="1"
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243 label="P-Value Adjusted Threshold"
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244 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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245 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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246 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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247 <option value="BY">Benjamini and Yekutieli (2001)</option>
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248 <option value="holm">Holm (1979)</option>
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249 <option value="none">None</option>
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250 </param>
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251 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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252 <option value="TMM" selected="true">TMM</option>
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253 <option value="RLE">RLE</option>
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254 <option value="upperquartile">Upperquartile</option>
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255 <option value="none">None (Don't normalise)</option>
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256 </param>
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257 <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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258 <param name="lrtOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use Likelihood Ratio Test?" help="Use likelihood ratio test instead of quasi-likelihood F-test. Default: No"/>
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259 </section>
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260
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261 </inputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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262
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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263 <outputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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264 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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265 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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266 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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267 </collection>
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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268 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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269 <filter>out['rscript']</filter>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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270 </data>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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271 </outputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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272
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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273 <tests>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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274 <!-- Ensure report is output -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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275 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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276 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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277 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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278 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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279 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
280 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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281 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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282 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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283 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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284 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
285 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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286 <param name="contrast" value="WT-Mut" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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287 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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288 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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289 <output_collection name="outTables" count="2">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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290 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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291 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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292 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
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293 <has_text_matching expression="11304.*0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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294 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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diff changeset
295 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
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296 <element name="edgeR_WT-Mut" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
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297 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
298 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
299 <has_text_matching expression="11304.*-0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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300 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
301 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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302 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
303 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
304 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
305 <has_text text="edgeR Analysis Output" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
306 <has_text text="quasi-likelihood" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
307 <not_has_text text="likelihood ratio" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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308 <not_has_text text="RData" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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309 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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310 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
311 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
312 <!-- Ensure annotation file input works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
313 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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314 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
315 <param name="annoOpt" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
316 <param name="geneanno" value="anno.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
317 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
318 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
319 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
320 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
321 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
322 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
323 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
324 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
325 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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326 <output_collection name="outTables" count="1">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
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327 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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328 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
329 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
330 <has_text_matching expression="11304.*Abca4.*0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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331 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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332 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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333 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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334 </test>
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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335 <!-- Ensure RScript and RData file can be output -->
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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336 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
337 <param name="format" value="matrix" />
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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338 <param name="rscript" value="True"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
339 <param name="rdaOption" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
340 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
341 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
342 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
343 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
344 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
345 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
346 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
347 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
348 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
349 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
350 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
351 <has_text text="RData" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
352 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
353 </output>
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
354 <output name="rscript" value="out_rscript.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
355 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
356 <!-- Ensure secondary factors work -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
357 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
358 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
359 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
360 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
361 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
362 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
363 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
364 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
365 <param name="factorName" value="Batch"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
366 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
367 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
368 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
369 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
370 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
371 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
372 <output_collection name="outTables" count="1" >
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
373 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
374 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
375 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
376 <has_text_matching expression="11304.*0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
377 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
378 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
379 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
380 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
381 <!-- Ensure factors file input works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
382 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
383 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
384 <param name="ffile" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
385 <param name="finfo" value="factorinfo.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
386 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
387 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
388 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
389 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
390 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
391 <output_collection name="outTables" count="1">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
392 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
393 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
394 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
395 <has_text_matching expression="11304.*0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
396 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
397 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
398 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
399 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
400 <!-- Ensure normalised counts file output works-->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
401 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
402 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
403 <param name="normCounts" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
404 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
405 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
406 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
407 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
408 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
409 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
410 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
411 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
412 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
413 <output_collection name="outTables" count="2">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
414 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
415 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
416 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
417 <has_text_matching expression="11304.*0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
418 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
419 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
420 <element name="edgeR_normcounts" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
421 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
422 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
423 <has_text_matching expression="11304.*15.7535" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
424 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
425 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
426 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
427 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
428 <!-- Ensure likelihood ratio option works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
429 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
430 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
431 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
432 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
433 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
434 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
435 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
436 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
437 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
438 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
439 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
440 <param name="lrtOption" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
441 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
442 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
443 <has_text text="likelihood ratio" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
444 <not_has_text text="quasi-likelihood" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
445 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
446 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
447 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
448 <!-- Ensure multiple counts files input works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
449 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
450 <param name="format" value="files" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
451 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
452 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
453 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
454 <param name="groupName" value="WT"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
455 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
456 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
457 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
458 <param name="groupName" value="Mut"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
459 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
460 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
461 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
462 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
463 <param name="factorName" value="Batch"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
464 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
465 <param name="groupName" value="b1"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
466 <param name="countsFile" value="WT1.counts,Mut1.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
467 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
468 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
469 <param name="groupName" value="b2"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
470 <param name="countsFile" value="WT2.counts,Mut2.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
471 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
472 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
473 <param name="groupName" value="b3"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
474 <param name="countsFile" value="WT3.counts,Mut3.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
475 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
476 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
477 <param name="annoOpt" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
478 <param name="geneanno" value="anno.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
479 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
480 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
481 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
482 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
483 <param name="contrast" value="WT-Mut" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
484 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
485 <param name="normCounts" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
486 <output_collection name="outTables" count="3">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
487 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
488 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
489 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
490 <has_text_matching expression="11304.*Abca4.*0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
491 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
492 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
493 <element name="edgeR_WT-Mut" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
494 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
495 <has_text_matching expression="logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
496 <has_text_matching expression="11304.*Abca4.*-0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
497 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
498 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
499 <element name="edgeR_normcounts" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
500 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
501 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
502 <has_text_matching expression="11304.*Abca4.*15.7535" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
503 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
504 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
505 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
506 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
507 <!-- Ensure filtering on CPM in Mnimum Samples works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
508 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
509 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
510 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
511 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
512 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
513 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
514 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
515 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
516 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
517 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
518 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
519 <param name="filt_select" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
520 <param name="format_select" value="cpm" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
521 <!-- real cpmReq values would be a lot lower
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
522 this is just for this tiny test dataset -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
523 <param name="cpmReq" value="1000" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
524 <param name="cpmSampleReq" value="3" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
525 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
526 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
527 <has_text text="CPM in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
528 <not_has_text text="after summing counts for all samples" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
529 <not_has_text text="counts in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
530 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
531 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
532 <output_collection name="outTables" count="1" >
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
533 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
534 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
535 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
536 <has_text_matching expression="11304.*0.4568" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
537 <not_has_text text="-0.0682" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
538 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
539 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
540 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
541 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
542 <!-- Ensure filtering on Count in Minmum Samples works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
543 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
544 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
545 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
546 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
547 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
548 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
549 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
550 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
551 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
552 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
553 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
554 <param name="filt_select" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
555 <param name="format_select" value="counts" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
556 <param name="cntReq" value="10" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
557 <param name="count_select" value="sample" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
558 <param name="cntSampleReq" value="3" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
559 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
560 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
561 <has_text text="counts in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
562 <not_has_text text="after summing counts for all samples" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
563 <not_has_text text="CPM in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
564 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
565 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
566 <output_collection name="outTables" count="1" >
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
567 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
568 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
569 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
570 <has_text_matching expression="11304.*0.4568" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
571 <not_has_text text="-0.0682" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
572 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
573 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
574
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
575 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
576 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
577 <!-- Ensure filtering on Total Count works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
578 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
579 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
580 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
581 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
582 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
583 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
584 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
585 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
586 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
587 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
588 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
589 <param name="filt_select" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
590 <param name="format_select" value="counts" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
591 <!-- real cntReq values would be a lot lower
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
592 this is just for this tiny test dataset -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
593 <param name="cntReq" value="1000" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
594 <param name="count_select" value="total" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
595 <param name="totReq" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
596 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
597 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
598 <has_text text="after summing counts for all samples" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
599 <not_has_text text="counts in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
600 <not_has_text text="CPM in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
601 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
602 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
603 <output_collection name="outTables" count="1" >
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
604 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
605 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
606 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
607 <has_text_matching expression="11304.*0.4568" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
608 <not_has_text text="-0.0682" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
609 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
610 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
611 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
612 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
613 </tests>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
614
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
615 <help><![CDATA[
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
616 .. class:: infomark
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
617
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
618 **What it does**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
619
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
620 Given a counts matrix, or a set of counts files, for example from **featureCounts**, and optional information about the genes, this tool
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
621 produces plots and tables useful in the analysis of differential gene expression.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
622
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623 This tool uses the `edgeR`_ quasi-likelihood pipeline (edgeR-quasi) for differential expression analysis. This statistical methodology uses negative binomial generalized linear models, but with F-tests instead of likelihood ratio tests. This method provides stricter error rate control than other negative binomial based pipelines, including the traditional edgeR pipelines or DESeq2. While the limma pipelines are recommended for large-scale datasets, because of their speed and flexibility, the edgeR-quasi pipeline gives better performance in low-count situations. For the data analyzed in this `edgeR workflow article`_ ,the edgeR-quasi, limma-voom and limma-trend pipelines are all equally suitable and give similar results.
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624
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625 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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626 .. _edgeR workflow article: https://f1000research.com/articles/5-1438
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627
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628 -----
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629
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630 **Inputs**
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631
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632 **Counts Data:**
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633
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634 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
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635
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636 Example - **Separate Count Files**:
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637
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638 ========== =======
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639 **GeneID** **WT1**
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640 ---------- -------
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641 11287 1699
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642 11298 1905
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643 11302 6
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644 11303 2099
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645 11304 356
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646 11305 2528
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647 ========== =======
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648
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649 Example - **Single Count Matrix**:
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650
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651 ========== ======= ======= ======= ======== ======== ========
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652 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
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653 ---------- ------- ------- ------- -------- -------- --------
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654 11287 1699 1528 1601 1463 1441 1495
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655 11298 1905 1744 1834 1345 1291 1346
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656 11302 6 8 7 5 6 5
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657 11303 2099 1974 2100 1574 1519 1654
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658 11304 356 312 337 361 397 346
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659 11305 2528 2438 2493 1762 1942 2027
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660 ========== ======= ======= ======= ======== ======== ========
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661
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662 **Factor Information:**
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663 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
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664
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665 Example:
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666
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667 ========== ============ =========
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668 **Sample** **Genotype** **Batch**
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669 ---------- ------------ ---------
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670 WT1 WT b1
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671 WT2 WT b2
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672 WT3 WT b3
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673 Mut1 Mut b1
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674 Mut2 Mut b2
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675 Mut3 Mut b3
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676 ========== ============ =========
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677
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678 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
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679
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680 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
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681
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682
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683 **Gene Annotations:**
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684 Optional input for gene annotations, this can contain more
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685 information about the genes than just an ID number. The annotations will
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686 be available in the differential expression results table and the optional normalised counts table.
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687
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688 Example:
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689
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690 ========== ========== ===================================================
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691 **GeneID** **Symbol** **GeneName**
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692 ---------- ---------- ---------------------------------------------------
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693 1287 Pzp pregnancy zone protein
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694 1298 Aanat arylalkylamine N-acetyltransferase
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695 1302 Aatk apoptosis-associated tyrosine kinase
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696 1303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
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697 1304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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698 1305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
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699 ========== ========== ===================================================
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700
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701 **Contrasts of Interest:**
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702 The contrasts you wish to make between levels.
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703 A common contrast would be a simple difference between two levels: "Mut-WT"
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704 represents the difference between the mutant and wild type genotypes.
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705 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
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706
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707 **Filter Low Counts:**
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708 Genes with very low counts across all libraries provide little evidence for differential expression.
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709 In the biological point of view, a gene must be expressed at some minimal level before
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710 it is likely to be translated into a protein or to be biologically important. In addition, the
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711 pronounced discreteness of these counts interferes with some of the statistical approximations
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712 that are used later in the pipeline. These genes should be filtered out prior to further
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
713 analysis.
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iuc
parents:
diff changeset
714 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
715 for any of the conditions. Users can set their own definition of genes being expressed. Usually
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
716 a gene is required to have a count of 5-10 in a library to be considered expressed in that
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
717 library. Users should also filter with count-per-million (CPM) rather than filtering on the
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
718 counts directly, as the latter does not account for differences in library sizes between samples.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
719
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
720 Option to ignore the genes that do not show significant levels of
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
721 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:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
722
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parents:
diff changeset
723 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
724 least the number of samples specified under Minimum Samples.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
725
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diff changeset
726 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
727 on Total Count or Minimum Samples.
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iuc
parents:
diff changeset
728
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
729 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
730 with a minimum total read count.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
731
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
732 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
733 requirement must be met in order for that gene to be kept.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
734
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
735 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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
736 ensure that the sample requirement is appropriate. In the case of an experiment
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
737 with two experimental groups each with two members, if there is a change from
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
738 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
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iuc
parents:
diff changeset
739 then this will cause that gene to fail the criteria. When in doubt simply do not
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
740 filter or consult the `edgeR workflow article`_ for filtering recommendations.
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parents:
diff changeset
741
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parents:
diff changeset
742 **Advanced Options:**
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parents:
diff changeset
743
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diff changeset
744 By default error rate for multiple testing is controlled using Benjamini and
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
745 Hochberg's false discovery rate control at a threshold value of 0.05. However
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
746 there are options to change this to custom values.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
747
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diff changeset
748 * **Minimum log2-fold-change Required:**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
749 In addition to meeting the requirement for the adjusted statistic for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
750 multiple testing, the observation must have an absolute log2-fold-change
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
751 greater than this threshold to be considered significant, thus highlighted
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
752 in the MD plot.
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diff changeset
753
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parents:
diff changeset
754 * **Adjusted Threshold:**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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755 Set the threshold for the resulting value of the multiple testing control
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parents:
diff changeset
756 method. Only observations whose statistic falls below this value is
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
757 considered significant, thus highlighted in the MD plot.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
758
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diff changeset
759 * **P-Value Adjustment Method:**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
760 Change the multiple testing control method, the options are BH(1995) and
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
761 BY(2001) which are both false discovery rate controls. There is also
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
762 Holm(1979) which is a method for family-wise error rate control.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
763
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
764 **Normalisation Method:**
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parents:
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765 The most obvious technical factor that affects the read counts, other than gene expression
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
766 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
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767 analysis for varying sequencing depths as represented by differing library sizes. This is
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
768 part of the basic modeling procedure and flows automatically into fold-change or p-value
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
769 calculations. It is always present, and doesn’t require any user intervention.
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770 The second most important technical influence on differential expression is one that is less
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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771 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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diff changeset
772 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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773 This commonly becomes important when a small number of genes are very highly expressed
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774 in one sample, but not in another. The highly expressed genes can consume a substantial
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775 proportion of the total library size, causing the remaining genes to be under-sampled in that
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
776 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
777 appear to be down-regulated in that sample . The edgeR `calcNormFactors` function normalizes for RNA composition by finding a set of scaling factors for the library sizes that minimize the log-fold changes between the samples for most genes. The default method for computing these scale factors uses a trimmed mean of M values (TMM) between each pair of samples. We call the product of the original library size and the scaling factor the *effective library size*. The effective library size replaces the original library size in all downsteam analyses. TMM is the recommended method for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. You can change the normalisation method under **Advanced Options** above. For more information, see the `calcNormFactors` section in the `edgeR User's Guide`_.
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778
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779 **Robust Settings**
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780 Option to use robust settings. Using robust settings (robust=TRUE) with the edgeR estimateDisp and glmQLFit functions is usually recommended to protect against outlier genes. This is turned on by default. Note that it is only used with the quasi-likelihood F test method. For more information, see the `edgeR workflow article`_.
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diff changeset
781
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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782 **Test Method**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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783 Option to use the likelihood ratio test instead of the quasi-likelihood F test. For more information, see the `edgeR workflow article`_.
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784
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785 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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786
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parents:
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787 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
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788
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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789 **Outputs**
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790
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parents:
diff changeset
791 This tool outputs
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parents:
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792
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793 * a table of differentially expressed genes for each contrast of interest
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794 * a HTML report with plots and additional information
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795
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796 Optionally, under **Output Options** you can choose to output
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797
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798 * a normalised counts table
2
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diff changeset
799 * the R script used by this tool
0
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800 * an RData file
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801
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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802 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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803
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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804 **Citations**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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805
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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806 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. For the edgeR method itself, please cite Robinson et al., 2010, and for this tool (which was developed from the Galaxy limma-voom tool) please cite Liu et al., 2015.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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807
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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808 ]]></help>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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809 <citations>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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810 <citation type="doi">10.1093/bioinformatics/btp616</citation>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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811 <citation type="doi">10.1093/nar/gkv412</citation>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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812 </citations>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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813 </tool>