annotate edger.xml @ 14:070900306913 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
author iuc
date Wed, 11 Oct 2023 11:13:07 +0000
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children 5bf899c13979
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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@">3</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 #if $formula:
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72 -F '$formula'
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73 #end if
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74
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75 #if $contrasts.contrastOpt == 'file':
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76 -C '$contrasts.cinfo'
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77 #else:
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78 -C '${ ','.join( ['%s' % $x.contrast for x in $contrasts.rep_contrast] ) }'
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79 #end if
0
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80
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81 #if $f.filt.filt_select == 'yes':
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82 #if $f.filt.cformat.format_select == 'cpm':
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83 -c '$f.filt.cformat.cpmReq'
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84 -s '$f.filt.cformat.cpmSampleReq'
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85 #elif $f.filt.cformat.format_select == 'counts':
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86 -z '$f.filt.cformat.cntReq'
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diff changeset
87 #if $f.filt.cformat.samples.count_select == 'total':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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88 -y
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
89 #elif $f.filt.cformat.samples.count_select == 'sample':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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90 -s '$f.filt.cformat.samples.cntSampleReq'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
91 #end if
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92 #end if
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93 #end if
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94
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diff changeset
95 #if $out.normCounts:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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96 -x
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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97 #end if
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98 #if $out.rdaOption:
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99 -r
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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100 #end if
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101
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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102 -l '$adv.lfc'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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103 -p '$adv.pVal'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
104 -d '$adv.pAdjust'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
105 -n '$adv.normalisationOption'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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106 #if $adv.robOption:
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parents:
diff changeset
107 -b
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
108 #end if
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109 #if $adv.lrtOption:
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parents:
diff changeset
110 -t
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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111 #end if
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parents:
diff changeset
112
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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113 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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114 mkdir ./output_dir
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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115
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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116 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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117 cp '$outReport.files_path'/*.tsv output_dir/
2
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parents: 1
diff changeset
118
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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parents: 1
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119 #if $out.rscript:
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120 && cp '$__tool_directory__/edger.R' '$rscript'
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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121 #end if
0
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122 ]]></command>
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123 <inputs>
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124 <!-- Counts and Factors -->
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125 <conditional name="input">
12
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126 <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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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127 <option value="files">Separate Count Files</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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128 <option value="matrix">Single Count Matrix</option>
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129 </param>
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130 <when value="files">
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131 <repeat name="rep_factor" title="Factor" min="1">
6
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132 <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
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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diff changeset
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>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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137 </sanitizer>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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138 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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139 <repeat name="rep_group" title="Group" min="2" default="2">
12
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140 <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
diff changeset
141 <sanitizer>
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142 <valid initial="string.letters,string.digits">
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parents: 11
diff changeset
143 <add value="_"/>
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parents: 11
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144 </valid>
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145 </sanitizer>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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146 </param>
3
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parents: 2
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147 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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148 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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149 </repeat>
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150 </when>
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151 <when value="matrix">
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152 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
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153 <conditional name="fact">
12
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154 <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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155 <option value="no">No</option>
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156 <option value="yes">Yes</option>
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157 </param>
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158 <when value="yes">
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159 <param name="finfo" type="data" format="tabular" label="Factor File"/>
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160 </when>
12
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161 <when value="no">
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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162 <repeat name="rep_factor" title="Factor" min="1">
12
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diff changeset
163 <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">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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parents: 11
diff changeset
164 <validator type="empty_field"/>
0
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165 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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166 </param>
12
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167 <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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diff changeset
168 <validator type="empty_field"/>
0
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169 <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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170 </param>
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171 </repeat>
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172 </when>
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173 </conditional>
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174 </when>
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175 </conditional>
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176 <!-- Gene Annotations -->
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177 <conditional name="anno">
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178 <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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179 <option value="no">No</option>
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180 <option value="yes">Yes</option>
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181 </param>
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182 <when value="yes">
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183 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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184 </when>
12
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185 <when value="no"/>
0
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186 </conditional>
14
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187 <!-- Optional formula -->
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188 <param name="formula" type="text" optional="true" label="Formula for linear model" help="An optional formula for the EdgeR linear model, this will override the use of the fields in factors as a simple sum. The formula can only use elements available in the factors file. This needs to be exactly as EdgeR expect the formula, ie. `~ 0 + factor_A + factor_B:factor_C`. See EdgeR documentation for more details.">
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189 <sanitizer invalid_char="">
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190 <valid initial="string.letters,string.digits">
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191 <add value="_"/>
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192 <add value="-"/>
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193 <add value="+"/>
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194 <add value="*"/>
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195 <add value="/"/>
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196 <add value="^"/>
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197 <add value=":"/>
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198 <add value="."/>
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199 <add value="~"/>
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200 <add value=" "/>
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201 <add value="("/>
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202 <add value=")"/>
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203 <add value="@"/>
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204 <add value="$"/>
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205 </valid>
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206 </sanitizer>
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207 </param>
0
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208 <!-- Contrasts -->
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209 <conditional name="contrasts">
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210 <param name="contrastOpt" type="select" label="Input contrasts manually or through a file">
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211 <option value="manual">manually</option>
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212 <option value="file">file</option>
0
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213 </param>
14
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214 <when value="manual">
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215 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
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216 <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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217 <validator type="empty_field"/>
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218 <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator>
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219 </param>
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220 </repeat>
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221 </when>
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222 <when value="file">
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223 <param name="cinfo" optional="true" type="data" format="tabular" label="Contrasts File" help="Setting this file will ignore any manually added contrasts above, make sure to remove any contrast fields above pressing the trash bin icon, or the tool will fail. First line of the file must be a header, below that each separate contrast should be on a line. Contrast formulas need to be based on ther factors data and potentially the formula provided. See EdgeR documentation on contrasts for more details."/>
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224 </when>
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225 </conditional>
0
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226 <!-- Filter Options -->
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227 <section name="f" expanded="false" title="Filter Low Counts">
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228 <conditional name="filt">
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229 <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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230 <option value="no" selected="true">No</option>
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231 <option value="yes">Yes</option>
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232 </param>
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233 <when value="yes">
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234 <conditional name="cformat">
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235 <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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236 <option value="cpm">CPM</option>
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237 <option value="counts">Counts</option>
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238 </param>
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239 <when value="cpm">
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240 <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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241 <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."/>
0
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242 </when>
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243 <when value="counts">
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244 <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."/>
0
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245 <conditional name="samples">
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246 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?">
0
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247 <option value="total">Total</option>
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248 <option value="sample">Sample</option>
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249 </param>
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df0c8d0a5992 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
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250 <when value="total"/>
0
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251 <when value="sample">
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252 <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."/>
0
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253 </when>
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254 </conditional>
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255 </when>
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256 </conditional>
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257 </when>
12
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258 <when value="no"/>
0
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259 </conditional>
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260 </section>
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261 <!-- Output Options -->
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262 <section name="out" expanded="false" title="Output Options">
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263 <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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264 </param>
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265 <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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266 <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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267 </param>
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268 </section>
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269 <!-- Advanced Options -->
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270 <section name="adv" expanded="false" title="Advanced Options">
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271 <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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272 <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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273 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
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274 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
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275 <option value="BY">Benjamini and Yekutieli (2001)</option>
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276 <option value="holm">Holm (1979)</option>
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277 <option value="none">None</option>
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278 </param>
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279 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
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280 <option value="TMM" selected="true">TMM</option>
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281 <option value="RLE">RLE</option>
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282 <option value="upperquartile">Upperquartile</option>
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283 <option value="none">None (Don't normalise)</option>
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284 </param>
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285 <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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286 <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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287 </section>
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288 </inputs>
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289 <outputs>
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290 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report"/>
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291 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
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292 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false"/>
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293 </collection>
2
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294 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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295 <filter>out['rscript']</filter>
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296 </data>
0
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297 </outputs>
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298 <tests>
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299 <!-- Ensure report is output -->
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300 <test expect_num_outputs="2">
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301 <param name="format" value="matrix"/>
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302 <param name="counts" value="matrix.txt"/>
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303 <repeat name="rep_factor">
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304 <param name="factorName" value="Genotype"/>
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305 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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306 </repeat>
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307 <param name="contrastOpt" value="manual"/>
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308 <repeat name="rep_contrast">
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309 <param name="contrast" value="Mut-WT"/>
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310 </repeat>
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311 <repeat name="rep_contrast">
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312 <param name="contrast" value="WT-Mut"/>
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313 </repeat>
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314 <param name="normalisationOption" value="TMM"/>
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315 <output_collection name="outTables" count="2">
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316 <element name="edgeR_Mut-WT" ftype="tabular">
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317 <assert_contents>
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318 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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319 <has_text_matching expression="11304.*0.4582"/>
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320 </assert_contents>
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321 </element>
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322 <element name="edgeR_WT-Mut" ftype="tabular">
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323 <assert_contents>
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324 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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325 <has_text_matching expression="11304.*-0.4582"/>
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326 </assert_contents>
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327 </element>
0
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328 </output_collection>
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329 <output name="outReport">
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330 <assert_contents>
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331 <has_text text="edgeR Analysis Output"/>
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332 <has_text text="quasi-likelihood"/>
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333 <not_has_text text="likelihood ratio"/>
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334 <not_has_text text="RData"/>
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335 </assert_contents>
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336 </output>
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337 </test>
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338 <!-- Complex contrasts constructions -->
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339 <test expect_num_outputs="2">
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340 <param name="format" value="matrix"/>
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341 <param name="counts" value="matrix-complex.txt"/>
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342 <repeat name="rep_factor">
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343 <param name="factorName" value="Genotype"/>
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344 <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB"/>
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345 </repeat>
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346 <param name="contrastOpt" value="manual"/>
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347 <repeat name="rep_contrast">
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348 <param name="contrast" value="(MutA-MutB)-(WTA-WTB)"/>
7
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349 </repeat>
12
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350 <param name="normalisationOption" value="TMM"/>
7
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351 <output_collection name="outTables" count="1">
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352 <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular">
7
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353 <assert_contents>
12
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354 <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
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355 <has_text_matching expression="11304.*15.53"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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356 </assert_contents>
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357 </element>
7
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358 </output_collection>
12
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359 <output name="outReport">
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360 <assert_contents>
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361 <has_text text="edgeR Analysis Output"/>
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362 <has_text text="quasi-likelihood"/>
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iuc
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363 <not_has_text text="likelihood ratio"/>
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364 <not_has_text text="RData"/>
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365 </assert_contents>
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366 </output>
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367 </test>
0
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368 <!-- Ensure annotation file input works -->
12
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369 <test expect_num_outputs="2">
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370 <param name="format" value="matrix"/>
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371 <param name="annoOpt" value="yes"/>
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iuc
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372 <param name="geneanno" value="anno.txt"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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373 <param name="counts" value="matrix.txt"/>
0
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374 <repeat name="rep_factor">
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375 <param name="factorName" value="Genotype"/>
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376 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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377 </repeat>
14
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diff changeset
378 <param name="contrastOpt" value="manual"/>
0
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379 <repeat name="rep_contrast">
12
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380 <param name="contrast" value="Mut-WT"/>
0
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381 </repeat>
12
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diff changeset
382 <param name="normalisationOption" value="TMM"/>
0
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383 <output_collection name="outTables" count="1">
12
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384 <element name="edgeR_Mut-WT" ftype="tabular">
2
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parents: 1
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385 <assert_contents>
12
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diff changeset
386 <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
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387 <has_text_matching expression="11304.*Abca4.*0.4582"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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388 </assert_contents>
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389 </element>
0
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390 </output_collection>
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391 </test>
2
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392 <!-- Ensure RScript and RData file can be output -->
12
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393 <test expect_num_outputs="3">
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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394 <param name="format" value="matrix"/>
2
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395 <param name="rscript" value="True"/>
12
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diff changeset
396 <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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397 <param name="counts" value="matrix.txt"/>
0
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398 <repeat name="rep_factor">
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399 <param name="factorName" value="Genotype"/>
12
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diff changeset
400 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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401 </repeat>
14
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parents: 13
diff changeset
402 <param name="contrastOpt" value="manual"/>
0
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diff changeset
403 <repeat name="rep_contrast">
12
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iuc
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diff changeset
404 <param name="contrast" value="Mut-WT"/>
0
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405 </repeat>
12
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parents: 11
diff changeset
406 <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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diff changeset
407 <output name="outReport">
0
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408 <assert_contents>
12
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diff changeset
409 <has_text text="RData"/>
0
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410 </assert_contents>
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411 </output>
4
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diff changeset
412 <output name="rscript">
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413 <assert_contents>
12
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diff changeset
414 <has_text_matching expression="Task run time"/>
4
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415 </assert_contents>
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416 </output>
0
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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 secondary factors work -->
12
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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="counts" value="matrix.txt"/>
0
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iuc
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diff changeset
422 <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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423 <param name="factorName" value="Genotype"/>
12
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diff changeset
424 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0
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diff changeset
425 </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
426 <repeat name="rep_factor">
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iuc
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diff changeset
427 <param name="factorName" value="Batch"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
428 <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
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429 </repeat>
14
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parents: 13
diff changeset
430 <param name="contrastOpt" value="manual"/>
0
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431 <repeat name="rep_contrast">
12
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parents: 11
diff changeset
432 <param name="contrast" value="Mut-WT"/>
0
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433 </repeat>
12
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parents: 11
diff changeset
434 <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
435 <output_collection name="outTables" count="1">
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diff changeset
436 <element name="edgeR_Mut-WT" ftype="tabular">
2
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iuc
parents: 1
diff changeset
437 <assert_contents>
12
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iuc
parents: 11
diff changeset
438 <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
439 <has_text_matching expression="11304.*0.4584"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
440 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
441 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
442 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
443 </test>
4
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents: 3
diff changeset
444 <!-- Ensure factors file with unordered samples works -->
12
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iuc
parents: 11
diff changeset
445 <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
446 <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
447 <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
448 <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
449 <param name="counts" value="matrix.txt"/>
14
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iuc
parents: 13
diff changeset
450 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
451 <repeat name="rep_contrast">
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="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
453 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
454 <param name="normalisationOption" value="TMM"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
455 <output_collection name="outTables" count="1">
12
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iuc
parents: 11
diff changeset
456 <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
457 <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
458 <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
459 <has_text_matching expression="11304.*0.4584"/>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
460 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
461 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
462 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
463 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
464 <!-- Ensure normalised counts file output works-->
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
465 <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
466 <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
467 <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
468 <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
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"/>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
471 <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
472 </repeat>
14
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
473 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
474 <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
475 <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
476 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
477 <param name="normalisationOption" value="TMM"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
478 <output_collection name="outTables" count="2">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
479 <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
480 <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
481 <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
482 <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
483 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
484 </element>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
485 <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
486 <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
487 <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
488 <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
489 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
490 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
491 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
492 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
493 <!-- 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
494 <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
495 <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
496 <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
497 <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
498 <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
499 <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
500 </repeat>
14
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
501 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
502 <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
503 <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
504 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
505 <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
506 <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
507 <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
508 <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
509 <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
510 <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
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diff changeset
511 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
512 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
513 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
514 <!-- 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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
523 <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
524 <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
525 <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
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diff changeset
526 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
527 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
528 <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
529 <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
530 <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
531 <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
532 <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
533 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
534 <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
535 <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
536 <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
537 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
538 <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
539 <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
540 <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
541 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
542 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
543 <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
544 <param name="geneanno" value="anno.txt"/>
14
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
545 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
546 <repeat name="rep_contrast">
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
547 <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
548 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
549 <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
550 <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
551 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
552 <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
553 <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
554 <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
555 <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
556 <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
557 <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
558 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
559 </element>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
560 <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
561 <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
562 <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
563 <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
564 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
565 </element>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
566 <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
567 <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
568 <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
569 <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
570 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
571 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
572 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
573 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
574 <!-- 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
575 <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
576 <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
577 <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
578 <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
579 <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
580 <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
581 </repeat>
14
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
582 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
583 <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
584 <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
585 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
586 <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
587 <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
588 <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
589 <!-- 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
590 this is just for this tiny test dataset -->
12
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iuc
parents: 11
diff changeset
591 <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
592 <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
593 <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
594 <assert_contents>
12
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iuc
parents: 11
diff changeset
595 <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
596 <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
597 <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
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diff changeset
598 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
599 </output>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
600 <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
601 <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
602 <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
603 <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
604 <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
605 <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
606 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
607 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
608 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
609 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
610 <!-- Ensure filtering on Count in Minmum Samples works -->
12
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iuc
parents: 11
diff changeset
611 <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
612 <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
613 <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
614 <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
615 <param name="factorName" value="Genotype"/>
12
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parents: 11
diff changeset
616 <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
617 </repeat>
14
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iuc
parents: 13
diff changeset
618 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
619 <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
620 <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
621 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
622 <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
623 <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
624 <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
625 <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
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 <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
633 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
634 </output>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
642 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
643 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
644 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
645 <!-- 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
646 <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
647 <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
648 <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
649 <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
650 <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
651 <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
652 </repeat>
14
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
653 <param name="contrastOpt" value="manual"/>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
654 <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
655 <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
656 </repeat>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
657 <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
658 <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
659 <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
660 <!-- 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
661 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
662 <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
663 <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
664 <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
665 <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
666 <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
667 <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
668 <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
669 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
670 </output>
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
671 <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
672 <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
673 <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
674 <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
675 <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
676 <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
677 </assert_contents>
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 11
diff changeset
678 </element>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
679 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
680 </test>
14
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
681 <!-- Ensure formula and contrast file work -->
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
682 <test expect_num_outputs="2">
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
683 <param name="format" value="matrix"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
684 <param name="counts" value="matrix.txt"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
685 <repeat name="rep_factor">
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
686 <param name="factorName" value="Genotype"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
687 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
688 </repeat>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
689 <repeat name="rep_factor">
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
690 <param name="factorName" value="Batch"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
691 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
692 </repeat>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
693 <param name="contrastOpt" value="file"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
694 <param name="cinfo" value="contrasts_file.txt"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
695 <param name="formula" value="~ 0 + Genotype + Batch"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
696 <param name="normalisationOption" value="TMM"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
697 <output_collection name="outTables" count="2">
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
698 <element name="edgeR_Mut-WT" ftype="tabular">
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
699 <assert_contents>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
700 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
701 <has_text_matching expression="11304.*0.4584"/>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
702 </assert_contents>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
703 </element>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
704 <element name="edgeR_WT-Mut" ftype="tabular">
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
705 <assert_contents>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
iuc
parents: 13
diff changeset
706 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/>
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diff changeset
707 </assert_contents>
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774
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diff changeset
708 </element>
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diff changeset
709 </output_collection>
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diff changeset
710 </test>
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
711 </tests>
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diff changeset
712 <help><![CDATA[
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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713 .. class:: infomark
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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714
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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715 **What it does**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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716
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
717 Given a counts matrix, or a set of counts files, for example from **featureCounts**, and optional information about the genes, this tool
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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718 produces plots and tables useful in the analysis of differential gene expression.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
719
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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720 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.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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721
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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722 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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723 .. _edgeR workflow article: https://f1000research.com/articles/5-1438
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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724
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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725 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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726
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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727 **Inputs**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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728
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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729 **Counts Data:**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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730
6
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diff changeset
731 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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
732
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
733 Example - **Separate Count Files**:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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734
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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735 ========== =======
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
736 **GeneID** **WT1**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
737 ---------- -------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
738 11287 1699
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
739 11298 1905
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
740 11302 6
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
741 11303 2099
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
742 11304 356
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
743 11305 2528
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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744 ========== =======
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
745
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
746 Example - **Single Count Matrix**:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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747
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748 ========== ======= ======= ======= ======== ======== ========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
749 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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750 ---------- ------- ------- ------- -------- -------- --------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
751 11287 1699 1528 1601 1463 1441 1495
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
752 11298 1905 1744 1834 1345 1291 1346
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
753 11302 6 8 7 5 6 5
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
754 11303 2099 1974 2100 1574 1519 1654
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
755 11304 356 312 337 361 397 346
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
756 11305 2528 2438 2493 1762 1942 2027
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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757 ========== ======= ======= ======= ======== ======== ========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
758
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
759
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
760 **Gene Annotations:**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
761 Optional input for gene annotations, this can contain more
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
762 information about the genes than just an ID number. The annotations will
3
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diff changeset
763 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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diff changeset
764
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
765 Example:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
766
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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767 ========== ========== ===================================================
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
768 **GeneID** **Symbol** **GeneName**
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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769 ---------- ---------- ---------------------------------------------------
3
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parents: 2
diff changeset
770 11287 Pzp pregnancy zone protein
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
771 11298 Aanat arylalkylamine N-acetyltransferase
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
772 11302 Aatk apoptosis-associated tyrosine kinase
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
773 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
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diff changeset
774 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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diff changeset
775 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0
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776 ========== ========== ===================================================
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diff changeset
777
4
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diff changeset
778 **Factor Information:**
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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779 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.
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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diff changeset
780
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diff changeset
781 Example:
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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782
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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783 ========== ============ =========
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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diff changeset
784 **Sample** **Genotype** **Batch**
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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785 ---------- ------------ ---------
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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diff changeset
786 WT1 WT b1
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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787 WT2 WT b2
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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diff changeset
788 WT3 WT b3
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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diff changeset
789 Mut1 Mut b1
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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790 Mut2 Mut b2
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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diff changeset
791 Mut3 Mut b3
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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792 ========== ============ =========
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793
6
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diff changeset
794 *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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diff changeset
795
6
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796 *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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797
14
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798 **Formula:**
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799 By default the tool will construct a formula for modelling counts based on the contents of the factors files or the factors given.
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800 This can be overriden by directly providing the EdgeR formula in section named Formula.
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801
0
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802 **Contrasts of Interest:**
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803 The contrasts you wish to make between levels.
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804 A common contrast would be a simple difference between two levels: "Mut-WT"
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805 represents the difference between the mutant and wild type genotypes.
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806 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
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807
14
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808 Alternatively, you can specify a file with contrasts. The file must contain a header (it's value is irrelevant)
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809 and one contrast per line on the first column (other columns are ignored). If using this option, make sure to
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810 remove any contrast section from the manual part, or the tool will fail.
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811
0
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812 **Filter Low Counts:**
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813 Genes with very low counts across all libraries provide little evidence for differential expression.
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814 In the biological point of view, a gene must be expressed at some minimal level before
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815 it is likely to be translated into a protein or to be biologically important. In addition, the
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816 pronounced discreteness of these counts interferes with some of the statistical approximations
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817 that are used later in the pipeline. These genes should be filtered out prior to further
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818 analysis.
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819 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
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820 for any of the conditions. Users can set their own definition of genes being expressed. Usually
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821 a gene is required to have a count of 5-10 in a library to be considered expressed in that
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822 library. Users should also filter with count-per-million (CPM) rather than filtering on the
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823 counts directly, as the latter does not account for differences in library sizes between samples.
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824
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825 Option to ignore the genes that do not show significant levels of
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826 expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values:
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827
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828 * **Minimum CPM:** This is the minimum count per million that a gene must have in at
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829 least the number of samples specified under Minimum Samples.
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830
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831 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
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832 on Total Count or Minimum Samples.
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833
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834 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
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835 with a minimum total read count.
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836
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837 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
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838 requirement must be met in order for that gene to be kept.
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839
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840 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
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841 ensure that the sample requirement is appropriate. In the case of an experiment
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842 with two experimental groups each with two members, if there is a change from
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843 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
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844 then this will cause that gene to fail the criteria. When in doubt simply do not
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845 filter or consult the `edgeR workflow article`_ for filtering recommendations.
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846
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847 **Advanced Options:**
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848
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849 By default error rate for multiple testing is controlled using Benjamini and
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850 Hochberg's false discovery rate control at a threshold value of 0.05. However
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851 there are options to change this to custom values.
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852
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853 * **Minimum log2-fold-change Required:**
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854 In addition to meeting the requirement for the adjusted statistic for
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855 multiple testing, the observation must have an absolute log2-fold-change
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856 greater than this threshold to be considered significant, thus highlighted
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857 in the MD plot.
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858
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859 * **Adjusted Threshold:**
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860 Set the threshold for the resulting value of the multiple testing control
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861 method. Only observations whose statistic falls below this value is
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862 considered significant, thus highlighted in the MD plot.
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863
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864 * **P-Value Adjustment Method:**
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865 Change the multiple testing control method, the options are BH(1995) and
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866 BY(2001) which are both false discovery rate controls. There is also
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867 Holm(1979) which is a method for family-wise error rate control.
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868
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869 **Normalisation Method:**
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870 The most obvious technical factor that affects the read counts, other than gene expression
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871 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
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872 analysis for varying sequencing depths as represented by differing library sizes. This is
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873 part of the basic modeling procedure and flows automatically into fold-change or p-value
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874 calculations. It is always present, and doesn’t require any user intervention.
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875 The second most important technical influence on differential expression is one that is less
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876 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
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877 sample, but does not provide any measure of the total RNA output on a per-cell basis.
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878 This commonly becomes important when a small number of genes are very highly expressed
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879 in one sample, but not in another. The highly expressed genes can consume a substantial
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880 proportion of the total library size, causing the remaining genes to be under-sampled in that
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881 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
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882 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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883
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884 **Robust Settings**
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885 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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886
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887 **Test Method**
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888 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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889
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890 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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891
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892 -----
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893
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894 **Outputs**
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895
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896 This tool outputs
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897
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898 * a table of differentially expressed genes for each contrast of interest
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899 * a HTML report with plots and additional information
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900
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901 Optionally, under **Output Options** you can choose to output
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902
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903 * a normalised counts table
2
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904 * the R script used by this tool
0
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905 * an RData file
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906
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907 -----
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908
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909 **Citations**
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910
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911 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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912
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913 ]]></help>
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914 <citations>
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915 <citation type="doi">10.1093/bioinformatics/btp616</citation>
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916 <citation type="doi">10.1093/nar/gkv412</citation>
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917 </citations>
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918 </tool>