annotate edger.xml @ 12:a8305cf0c951 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
author iuc
date Thu, 21 Sep 2023 10:01:55 +0000
parents f2843df56434
children 0cb907a2a810
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1 <tool id="edger" name="edgeR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>
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3 Perform differential expression of count data
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4 </description>
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5 <macros>
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6 <token name="@TOOL_VERSION@">3.36.0</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
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8 </macros>
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9 <edam_topics>
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10 <edam_topic>topic_3308</edam_topic>
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11 </edam_topics>
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12 <edam_operations>
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13 <edam_operation>operation_3563</edam_operation>
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14 <edam_operation>operation_3223</edam_operation>
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15 </edam_operations>
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16 <xrefs>
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17 <xref type="bio.tools">edger</xref>
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18 <xref type="bioconductor">edger</xref>
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19 </xrefs>
0
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20 <requirements>
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21 <requirement type="package" version="@TOOL_VERSION@">bioconductor-edger</requirement>
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22 <requirement type="package" version="3.50.0">bioconductor-limma</requirement>
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23 <requirement type="package" version="0.2.20">r-rjson</requirement>
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24 <requirement type="package" version="1.20.3">r-getopt</requirement>
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25 <requirement type="package" version="1.4.36">r-statmod</requirement>
0
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26 <!-- required for alpha function used with plotMD -->
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27 <requirement type="package" version="1.1.1">r-scales</requirement>
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28 </requirements>
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29 <version_command><![CDATA[
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30 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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
0
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31 ]]></version_command>
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32 <command detect_errors="exit_code"><![CDATA[
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33 #import json
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34 Rscript '$__tool_directory__/edger.R'
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35
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36 -R '$outReport'
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37 -o '$outReport.files_path'
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38
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39 #if $input.format=="files":
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40
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41 ## Adapted from DESeq2 wrapper
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42 #set $temp_factor_names = list()
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43 #for $fact in $input.rep_factor:
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44 #set $temp_factor = list()
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45 #for $g in $fact.rep_group:
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46 #set $count_files = list()
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47 #for $file in $g.countsFile:
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48 $count_files.append(str($file))
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49 #end for
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50 $temp_factor.append( {str($g.groupName): $count_files} )
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51 #end for
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52
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53 $temp_factor.reverse()
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54 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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55 #end for
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56 -j '#echo json.dumps(temp_factor_names)#'
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57
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58 #elif $input.format=="matrix":
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59 -m '$input.counts'
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60 #if $input.fact.ffile=='yes':
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61 -f '$input.fact.finfo'
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62 #else:
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63 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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64 #end if
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65 #end if
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66
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67 #if $anno.annoOpt=='yes':
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68 -a '$anno.geneanno'
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69 #end if
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70
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71 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
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72
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73 #if $f.filt.filt_select == 'yes':
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74 #if $f.filt.cformat.format_select == 'cpm':
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75 -c '$f.filt.cformat.cpmReq'
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76 -s '$f.filt.cformat.cpmSampleReq'
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77 #elif $f.filt.cformat.format_select == 'counts':
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78 -z '$f.filt.cformat.cntReq'
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79 #if $f.filt.cformat.samples.count_select == 'total':
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80 -y
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81 #elif $f.filt.cformat.samples.count_select == 'sample':
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82 -s '$f.filt.cformat.samples.cntSampleReq'
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83 #end if
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84 #end if
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85 #end if
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86
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diff changeset
87 #if $out.normCounts:
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88 -x
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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89 #end if
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90 #if $out.rdaOption:
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91 -r
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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92 #end if
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93
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94 -l '$adv.lfc'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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95 -p '$adv.pVal'
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96 -d '$adv.pAdjust'
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97 -n '$adv.normalisationOption'
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98 #if $adv.robOption:
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99 -b
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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100 #end if
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101 #if $adv.lrtOption:
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102 -t
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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103 #end if
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104
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105 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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106 mkdir ./output_dir
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107
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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108 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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109 cp '$outReport.files_path'/*.tsv output_dir/
2
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parents: 1
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110
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111 #if $out.rscript:
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112 && cp '$__tool_directory__/edger.R' '$rscript'
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113 #end if
0
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114 ]]></command>
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115 <inputs>
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116 <!-- Counts and Factors -->
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117 <conditional name="input">
12
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118 <param name="format" type="select" label="Count Files or Matrix?" help="You can choose to input either separate count files (one per sample) or a single count matrix">
0
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119 <option value="files">Separate Count Files</option>
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120 <option value="matrix">Single Count Matrix</option>
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121 </param>
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122 <when value="files">
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123 <repeat name="rep_factor" title="Factor" min="1">
6
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124 <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, and the first character of each factor must be a letter">
12
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125 <sanitizer>
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126 <valid initial="string.letters,string.digits">
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127 <add value="_"/>
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128 </valid>
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129 </sanitizer>
0
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130 </param>
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131 <repeat name="rep_group" title="Group" min="2" default="2">
12
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132 <param name="groupName" type="text" label="Name" help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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parents: 11
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133 <sanitizer>
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134 <valid initial="string.letters,string.digits">
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135 <add value="_"/>
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136 </valid>
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137 </sanitizer>
0
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138 </param>
3
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139 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
0
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140 </repeat>
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141 </repeat>
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142 </when>
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143 <when value="matrix">
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144 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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145 <conditional name="fact">
12
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146 <param name="ffile" type="select" label="Input factor information from file?" help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each sample, factor and group must be a letter">
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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147 <option value="no">No</option>
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148 <option value="yes">Yes</option>
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149 </param>
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150 <when value="yes">
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151 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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152 </when>
12
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153 <when value="no">
0
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154 <repeat name="rep_factor" title="Factor" min="1">
12
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155 <param name="factorName" type="text" label="Factor 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. 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, and the first character of each factor must be a letter">
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156 <validator type="empty_field"/>
0
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157 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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158 </param>
12
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159 <param name="groupNames" type="text" label="Groups" 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), and the first character of each group must be a letter">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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160 <validator type="empty_field"/>
0
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161 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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162 </param>
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163 </repeat>
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164 </when>
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165 </conditional>
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166 </when>
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167 </conditional>
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168 <!-- Gene Annotations -->
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169 <conditional name="anno">
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170 <param name="annoOpt" type="select" label="Use Gene Annotations?" help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene. See Help section below.">
0
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171 <option value="no">No</option>
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172 <option value="yes">Yes</option>
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173 </param>
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174 <when value="yes">
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175 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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176 </when>
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177 <when value="no"/>
0
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178 </conditional>
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179 <!-- Contrasts -->
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180 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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181 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (MT.t1-MT.t0)-(WT.t1-WT.t0). 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 or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons.">
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182 <validator type="empty_field"/>
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183 <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator>
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184 </param>
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185 </repeat>
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186 <!-- Filter Options -->
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187 <section name="f" expanded="false" title="Filter Low Counts">
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188 <conditional name="filt">
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189 <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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190 <option value="no" selected="true">No</option>
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191 <option value="yes">Yes</option>
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192 </param>
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193 <when value="yes">
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194 <conditional name="cformat">
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195 <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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196 <option value="cpm">CPM</option>
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197 <option value="counts">Counts</option>
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198 </param>
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199 <when value="cpm">
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200 <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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201 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" 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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202 </when>
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203 <when value="counts">
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204 <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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205 <conditional name="samples">
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206 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?">
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207 <option value="total">Total</option>
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208 <option value="sample">Sample</option>
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209 </param>
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210 <when value="total"/>
0
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211 <when value="sample">
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212 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" 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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213 </when>
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214 </conditional>
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215 </when>
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216 </conditional>
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217 </when>
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218 <when value="no"/>
0
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219 </conditional>
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220 </section>
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221 <!-- Output Options -->
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222 <section name="out" expanded="false" title="Output Options">
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223 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output Normalised Counts Table?" help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
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224 </param>
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225 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
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226 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output RData file?" 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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227 </param>
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228 </section>
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229 <!-- Advanced Options -->
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230 <section name="adv" expanded="false" title="Advanced Options">
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231 <param name="lfc" type="float" value="0" min="0" label="Minimum Log2 Fold Change" 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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232 <param name="pVal" type="float" value="0.05" min="0" max="1" label="P-Value Adjusted Threshold" 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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233 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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234 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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235 <option value="BY">Benjamini and Yekutieli (2001)</option>
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236 <option value="holm">Holm (1979)</option>
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237 <option value="none">None</option>
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238 </param>
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239 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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240 <option value="TMM" selected="true">TMM</option>
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241 <option value="RLE">RLE</option>
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242 <option value="upperquartile">Upperquartile</option>
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243 <option value="none">None (Don't normalise)</option>
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244 </param>
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245 <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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246 <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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247 </section>
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248 </inputs>
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249 <outputs>
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250 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report"/>
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251 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
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252 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false"/>
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253 </collection>
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254 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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255 <filter>out['rscript']</filter>
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256 </data>
0
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257 </outputs>
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258 <tests>
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259 <!-- Ensure report is output -->
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260 <test expect_num_outputs="2">
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261 <param name="format" value="matrix"/>
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262 <param name="counts" value="matrix.txt"/>
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263 <repeat name="rep_factor">
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264 <param name="factorName" value="Genotype"/>
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265 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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266 </repeat>
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267 <repeat name="rep_contrast">
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268 <param name="contrast" value="Mut-WT"/>
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269 </repeat>
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270 <repeat name="rep_contrast">
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271 <param name="contrast" value="WT-Mut"/>
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272 </repeat>
12
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273 <param name="normalisationOption" value="TMM"/>
0
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274 <output_collection name="outTables" count="2">
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275 <element name="edgeR_Mut-WT" ftype="tabular">
2
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276 <assert_contents>
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277 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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278 <has_text_matching expression="11304.*0.4582"/>
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279 </assert_contents>
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280 </element>
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281 <element name="edgeR_WT-Mut" ftype="tabular">
2
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282 <assert_contents>
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283 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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284 <has_text_matching expression="11304.*-0.4582"/>
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285 </assert_contents>
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286 </element>
0
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287 </output_collection>
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288 <output name="outReport">
0
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289 <assert_contents>
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290 <has_text text="edgeR Analysis Output"/>
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291 <has_text text="quasi-likelihood"/>
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292 <not_has_text text="likelihood ratio"/>
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293 <not_has_text text="RData"/>
0
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294 </assert_contents>
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295 </output>
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296 </test>
7
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297 <!-- Complex contrasts constructions -->
12
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298 <test expect_num_outputs="2">
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299 <param name="format" value="matrix"/>
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300 <param name="counts" value="matrix-complex.txt"/>
7
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301 <repeat name="rep_factor">
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302 <param name="factorName" value="Genotype"/>
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303 <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB"/>
7
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304 </repeat>
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305 <repeat name="rep_contrast">
12
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306 <param name="contrast" value="(MutA-MutB)-(WTA-WTB)"/>
7
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307 </repeat>
12
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308 <param name="normalisationOption" value="TMM"/>
7
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309 <output_collection name="outTables" count="1">
12
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310 <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular">
7
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311 <assert_contents>
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312 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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313 <has_text_matching expression="11304.*15.53"/>
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314 </assert_contents>
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315 </element>
7
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316 </output_collection>
12
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317 <output name="outReport">
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318 <assert_contents>
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319 <has_text text="edgeR Analysis Output"/>
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320 <has_text text="quasi-likelihood"/>
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321 <not_has_text text="likelihood ratio"/>
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322 <not_has_text text="RData"/>
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323 </assert_contents>
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324 </output>
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325 </test>
0
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326 <!-- Ensure annotation file input works -->
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327 <test expect_num_outputs="2">
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328 <param name="format" value="matrix"/>
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329 <param name="annoOpt" value="yes"/>
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330 <param name="geneanno" value="anno.txt"/>
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331 <param name="counts" value="matrix.txt"/>
0
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332 <repeat name="rep_factor">
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333 <param name="factorName" value="Genotype"/>
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334 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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335 </repeat>
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336 <repeat name="rep_contrast">
12
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337 <param name="contrast" value="Mut-WT"/>
0
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338 </repeat>
12
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339 <param name="normalisationOption" value="TMM"/>
0
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340 <output_collection name="outTables" count="1">
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341 <element name="edgeR_Mut-WT" ftype="tabular">
2
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342 <assert_contents>
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343 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR"/>
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344 <has_text_matching expression="11304.*Abca4.*0.4582"/>
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345 </assert_contents>
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346 </element>
0
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347 </output_collection>
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348 </test>
2
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349 <!-- Ensure RScript and RData file can be output -->
12
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350 <test expect_num_outputs="3">
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351 <param name="format" value="matrix"/>
2
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352 <param name="rscript" value="True"/>
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353 <param name="rdaOption" value="true"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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354 <param name="counts" value="matrix.txt"/>
0
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355 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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356 <param name="factorName" value="Genotype"/>
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357 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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358 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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359 <repeat name="rep_contrast">
12
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360 <param name="contrast" value="Mut-WT"/>
0
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361 </repeat>
12
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iuc
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362 <param name="normalisationOption" value="TMM"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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363 <output name="outReport">
0
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364 <assert_contents>
12
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365 <has_text text="RData"/>
0
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366 </assert_contents>
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367 </output>
4
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368 <output name="rscript">
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369 <assert_contents>
12
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370 <has_text_matching expression="Task run time"/>
4
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iuc
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371 </assert_contents>
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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372 </output>
0
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373 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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374 <!-- Ensure secondary factors work -->
12
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iuc
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375 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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376 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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377 <param name="counts" value="matrix.txt"/>
0
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iuc
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diff changeset
378 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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379 <param name="factorName" value="Genotype"/>
12
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diff changeset
380 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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diff changeset
381 </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
382 <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
383 <param name="factorName" value="Batch"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
384 <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
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diff changeset
385 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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386 <repeat name="rep_contrast">
12
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iuc
parents: 11
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387 <param name="contrast" value="Mut-WT"/>
0
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388 </repeat>
12
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iuc
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diff changeset
389 <param name="normalisationOption" value="TMM"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
390 <output_collection name="outTables" count="1">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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diff changeset
391 <element name="edgeR_Mut-WT" ftype="tabular">
2
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parents: 1
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392 <assert_contents>
12
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diff changeset
393 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
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394 <has_text_matching expression="11304.*0.4584"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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395 </assert_contents>
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iuc
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396 </element>
0
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397 </output_collection>
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398 </test>
4
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parents: 3
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399 <!-- Ensure factors file with unordered samples works -->
12
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iuc
parents: 11
diff changeset
400 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
401 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
402 <param name="ffile" value="yes"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
403 <param name="finfo" value="factorinfo.txt"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
404 <param name="counts" value="matrix.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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405 <repeat name="rep_contrast">
12
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parents: 11
diff changeset
406 <param name="contrast" value="Mut-WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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407 </repeat>
12
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iuc
parents: 11
diff changeset
408 <param name="normalisationOption" value="TMM"/>
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
409 <output_collection name="outTables" count="1">
12
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parents: 11
diff changeset
410 <element name="edgeR_Mut-WT" ftype="tabular">
2
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parents: 1
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411 <assert_contents>
12
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parents: 11
diff changeset
412 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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413 <has_text_matching expression="11304.*0.4584"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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414 </assert_contents>
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iuc
parents: 11
diff changeset
415 </element>
0
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416 </output_collection>
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417 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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418 <!-- Ensure normalised counts file output works-->
12
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iuc
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diff changeset
419 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
420 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
421 <param name="normCounts" value="true"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
422 <param name="counts" value="matrix.txt"/>
0
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iuc
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diff changeset
423 <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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424 <param name="factorName" value="Genotype"/>
12
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parents: 11
diff changeset
425 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
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
426 </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
427 <repeat name="rep_contrast">
12
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iuc
parents: 11
diff changeset
428 <param name="contrast" value="Mut-WT"/>
0
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diff changeset
429 </repeat>
12
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iuc
parents: 11
diff changeset
430 <param name="normalisationOption" value="TMM"/>
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
431 <output_collection name="outTables" count="2">
12
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parents: 11
diff changeset
432 <element name="edgeR_Mut-WT" ftype="tabular">
2
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parents: 1
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433 <assert_contents>
12
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parents: 11
diff changeset
434 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
435 <has_text_matching expression="11304.*0.4582"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
436 </assert_contents>
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diff changeset
437 </element>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
438 <element name="edgeR_normcounts" ftype="tabular">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
439 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
440 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
441 <has_text_matching expression="11304.*15.75"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
442 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
443 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
444 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
445 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
446 <!-- Ensure likelihood ratio option works -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
447 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
448 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
449 <param name="counts" value="matrix.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
450 <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
451 <param name="factorName" value="Genotype"/>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
452 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
453 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
454 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
455 <param name="contrast" value="Mut-WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
456 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
457 <param name="normalisationOption" value="TMM"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
458 <param name="lrtOption" value="true"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
459 <output name="outReport">
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
460 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
461 <has_text text="likelihood ratio"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
462 <not_has_text text="quasi-likelihood"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
463 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
464 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
465 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
466 <!-- Ensure multiple counts files input works -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
467 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
468 <param name="format" value="files"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
469 <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
470 <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
471 <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
472 <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
473 <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
474 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
475 <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
476 <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
477 <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
478 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
479 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
480 <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
481 <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
482 <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
483 <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
484 <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
485 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
486 <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
487 <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
488 <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
489 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
490 <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
491 <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
492 <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
493 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
494 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
495 <param name="annoOpt" value="yes"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
496 <param name="geneanno" value="anno.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
497 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
498 <param name="contrast" value="Mut-WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
499 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
500 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
501 <param name="contrast" value="WT-Mut"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
502 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
503 <param name="normCounts" value="true"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
504 <output_collection name="outTables" count="3">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
505 <element name="edgeR_Mut-WT" ftype="tabular">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
506 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
507 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
508 <has_text_matching expression="11304.*Abca4.*0.4584"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
509 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
510 </element>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
511 <element name="edgeR_WT-Mut" ftype="tabular">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
512 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
513 <has_text_matching expression="logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
514 <has_text_matching expression="11304.*Abca4.*-0.4584"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
515 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
516 </element>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
517 <element name="edgeR_normcounts" ftype="tabular">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
518 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
519 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
520 <has_text_matching expression="11304.*Abca4.*15.75"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
521 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
522 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
523 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
524 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
525 <!-- Ensure filtering on CPM in Mnimum Samples works -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
526 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
527 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
528 <param name="counts" value="matrix.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
529 <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
530 <param name="factorName" value="Genotype"/>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
531 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
532 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
533 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
534 <param name="contrast" value="Mut-WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
535 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
536 <param name="normalisationOption" value="TMM"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
537 <param name="filt_select" value="yes"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
538 <param name="format_select" value="cpm"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
539 <!-- 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
540 this is just for this tiny test dataset -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
541 <param name="cpmReq" value="1000"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
542 <param name="cpmSampleReq" value="3"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
543 <output name="outReport">
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
544 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
545 <has_text text="CPM in at least"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
546 <not_has_text text="after summing counts for all samples"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
547 <not_has_text text="counts in at least"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
548 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
549 </output>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
550 <output_collection name="outTables" count="1">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
551 <element name="edgeR_Mut-WT" ftype="tabular">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
552 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
553 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
554 <has_text_matching expression="11304.*0.4568"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
555 <not_has_text text="-0.0682"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
556 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
557 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
558 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
559 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
560 <!-- Ensure filtering on Count in Minmum Samples works -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
561 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
562 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
563 <param name="counts" value="matrix.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
564 <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
565 <param name="factorName" value="Genotype"/>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
566 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
567 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
568 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
569 <param name="contrast" value="Mut-WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
570 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
571 <param name="normalisationOption" value="TMM"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
572 <param name="filt_select" value="yes"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
573 <param name="format_select" value="counts"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
574 <param name="cntReq" value="10"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
575 <param name="count_select" value="sample"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
576 <param name="cntSampleReq" value="3"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
577 <output name="outReport">
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
578 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
579 <has_text text="counts in at least"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
580 <not_has_text text="after summing counts for all samples"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
581 <not_has_text text="CPM in at least"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
582 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
583 </output>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
584 <output_collection name="outTables" count="1">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
585 <element name="edgeR_Mut-WT" ftype="tabular">
2
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents: 1
diff changeset
586 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
587 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
588 <has_text_matching expression="11304.*0.4568"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
589 <not_has_text text="-0.0682"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
590 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
591 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
592 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
593 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
594 <!-- Ensure filtering on Total Count works -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
595 <test expect_num_outputs="2">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
596 <param name="format" value="matrix"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
597 <param name="counts" value="matrix.txt"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
598 <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
599 <param name="factorName" value="Genotype"/>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
600 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
601 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
602 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
603 <param name="contrast" value="Mut-WT"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
604 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
605 <param name="normalisationOption" value="TMM"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
606 <param name="filt_select" value="yes"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
607 <param name="format_select" value="counts"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
608 <!-- 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
609 this is just for this tiny test dataset -->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
610 <param name="cntReq" value="1000"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
611 <param name="count_select" value="total"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
612 <output name="outReport">
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
613 <assert_contents>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
614 <has_text text="after summing counts for all samples"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
615 <not_has_text text="counts in at least"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
616 <not_has_text text="CPM in at least"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
617 </assert_contents>
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618 </output>
12
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619 <output_collection name="outTables" count="1">
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620 <element name="edgeR_Mut-WT" ftype="tabular">
2
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621 <assert_contents>
12
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622 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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623 <has_text_matching expression="11304.*0.4568"/>
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624 <not_has_text text="-0.0682"/>
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625 </assert_contents>
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626 </element>
0
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627 </output_collection>
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628 </test>
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629 </tests>
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630 <help><![CDATA[
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631 .. class:: infomark
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632
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633 **What it does**
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634
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635 Given a counts matrix, or a set of counts files, for example from **featureCounts**, and optional information about the genes, this tool
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636 produces plots and tables useful in the analysis of differential gene expression.
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637
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638 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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639
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640 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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641 .. _edgeR workflow article: https://f1000research.com/articles/5-1438
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642
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643 -----
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644
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645 **Inputs**
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646
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647 **Counts Data:**
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648
6
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649 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
0
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650
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651 Example - **Separate Count Files**:
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652
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653 ========== =======
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654 **GeneID** **WT1**
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655 ---------- -------
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656 11287 1699
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657 11298 1905
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658 11302 6
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659 11303 2099
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660 11304 356
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661 11305 2528
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662 ========== =======
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663
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664 Example - **Single Count Matrix**:
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665
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666 ========== ======= ======= ======= ======== ======== ========
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667 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
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668 ---------- ------- ------- ------- -------- -------- --------
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669 11287 1699 1528 1601 1463 1441 1495
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670 11298 1905 1744 1834 1345 1291 1346
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671 11302 6 8 7 5 6 5
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672 11303 2099 1974 2100 1574 1519 1654
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673 11304 356 312 337 361 397 346
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674 11305 2528 2438 2493 1762 1942 2027
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675 ========== ======= ======= ======= ======== ======== ========
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676
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677
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678 **Gene Annotations:**
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679 Optional input for gene annotations, this can contain more
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680 information about the genes than just an ID number. The annotations will
3
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681 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
0
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682
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683 Example:
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684
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685 ========== ========== ===================================================
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686 **GeneID** **Symbol** **GeneName**
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687 ---------- ---------- ---------------------------------------------------
3
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688 11287 Pzp pregnancy zone protein
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689 11298 Aanat arylalkylamine N-acetyltransferase
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690 11302 Aatk apoptosis-associated tyrosine kinase
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691 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
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692 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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693 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0
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694 ========== ========== ===================================================
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695
4
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696 **Factor Information:**
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697 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
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698
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699 Example:
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700
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701 ========== ============ =========
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702 **Sample** **Genotype** **Batch**
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703 ---------- ------------ ---------
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704 WT1 WT b1
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705 WT2 WT b2
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706 WT3 WT b3
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707 Mut1 Mut b1
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708 Mut2 Mut b2
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diff changeset
709 Mut3 Mut b3
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diff changeset
710 ========== ============ =========
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711
6
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diff changeset
712 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered, the name should start with a letter and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
4
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713
6
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diff changeset
714 *Groups:* The names of the groups for the factor. The names should start with a letter, and only contain letters, numbers and underscores, other characters such as spaces and hyphens must not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas.
4
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diff changeset
715
0
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parents:
diff changeset
716 **Contrasts of Interest:**
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parents:
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717 The contrasts you wish to make between levels.
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parents:
diff changeset
718 A common contrast would be a simple difference between two levels: "Mut-WT"
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parents:
diff changeset
719 represents the difference between the mutant and wild type genotypes.
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parents:
diff changeset
720 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
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diff changeset
721
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parents:
diff changeset
722 **Filter Low Counts:**
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parents:
diff changeset
723 Genes with very low counts across all libraries provide little evidence for differential 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
724 In the biological point of view, a gene must be expressed at some minimal level before
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 it is likely to be translated into a protein or to be biologically important. In addition, the
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
726 pronounced discreteness of these counts interferes with some of the statistical approximations
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parents:
diff changeset
727 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
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diff changeset
728 analysis.
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diff changeset
729 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
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diff changeset
730 for any of the conditions. Users can set their own definition of genes being expressed. Usually
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diff changeset
731 a gene is required to have a count of 5-10 in a library to be considered expressed in that
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diff changeset
732 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
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diff changeset
733 counts directly, as the latter does not account for differences in library sizes between samples.
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diff changeset
734
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735 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
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diff changeset
736 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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diff changeset
737
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738 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
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739 least the number of samples specified under Minimum Samples.
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740
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741 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
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742 on Total Count or Minimum Samples.
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743
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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744 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
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745 with a minimum total read count.
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746
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747 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
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748 requirement must be met in order for that gene to be kept.
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749
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750 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
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diff changeset
751 ensure that the sample requirement is appropriate. In the case of an experiment
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752 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
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753 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
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754 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
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755 filter or consult the `edgeR workflow article`_ for filtering recommendations.
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756
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757 **Advanced Options:**
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758
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759 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
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760 Hochberg's false discovery rate control at a threshold value of 0.05. However
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761 there are options to change this to custom values.
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762
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763 * **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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764 In addition to meeting the requirement for the adjusted statistic for
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765 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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766 greater than this threshold to be considered significant, thus highlighted
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767 in the MD plot.
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768
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769 * **Adjusted Threshold:**
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770 Set the threshold for the resulting value of the multiple testing control
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771 method. Only observations whose statistic falls below this value is
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772 considered significant, thus highlighted in the MD plot.
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773
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774 * **P-Value Adjustment Method:**
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775 Change the multiple testing control method, the options are BH(1995) and
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776 BY(2001) which are both false discovery rate controls. There is also
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777 Holm(1979) which is a method for family-wise error rate control.
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778
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779 **Normalisation Method:**
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780 The most obvious technical factor that affects the read counts, other than gene expression
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781 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
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782 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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783 part of the basic modeling procedure and flows automatically into fold-change or p-value
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784 calculations. It is always present, and doesn’t require any user intervention.
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785 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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786 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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787 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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788 This commonly becomes important when a small number of genes are very highly expressed
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789 in one sample, but not in another. The highly expressed genes can consume a substantial
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790 proportion of the total library size, causing the remaining genes to be under-sampled in that
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791 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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792 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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793
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794 **Robust Settings**
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795 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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796
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797 **Test Method**
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798 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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799
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800 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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801
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802 -----
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803
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804 **Outputs**
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805
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806 This tool outputs
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807
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808 * a table of differentially expressed genes for each contrast of interest
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809 * a HTML report with plots and additional information
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810
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811 Optionally, under **Output Options** you can choose to output
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812
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813 * a normalised counts table
2
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814 * the R script used by this tool
0
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815 * an RData file
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816
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817 -----
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818
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819 **Citations**
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820
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821 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.
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822
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823 ]]></help>
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824 <citations>
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825 <citation type="doi">10.1093/bioinformatics/btp616</citation>
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826 <citation type="doi">10.1093/nar/gkv412</citation>
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827 </citations>
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828 </tool>