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annotate deseq2.xml @ 24:71bacea10eee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
author iuc
date Sat, 29 Feb 2020 17:08:08 -0500
parents e5c8afac22a7
children de44f8eff84a
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71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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1 <tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">
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2 <description>Determines differentially expressed features from count tables</description>
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3 <macros>
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4 <import>deseq2_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
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8 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
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9 <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
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10 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
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11 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
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12 <requirement type="package" version="1.20.2">r-getopt</requirement>
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13 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
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14 <requirement type="package" version="3.0.1">r-gplots</requirement>
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15 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
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16 <requirement type="package" version="0.2.20">r-rjson</requirement>
0
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17 </requirements>
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18 <stdio>
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19 <regex match="Execution halted"
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20 source="both"
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21 level="fatal"
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22 description="Execution halted." />
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23 <regex match="Error in"
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24 source="both"
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25 level="fatal"
7
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26 description="An undefined error occurred, please check your input carefully and contact your administrator." />
0
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27 <regex match="Fatal error"
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28 source="both"
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29 level="fatal"
7
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30 description="An undefined error occurred, please check your input carefully and contact your administrator." />
0
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31 </stdio>
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32 <version_command><![CDATA[
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33 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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34 ]]></version_command>
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35 <command><![CDATA[
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36 #if $tximport.tximport_selector == 'tximport':
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37 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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38 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
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39 #else:
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40 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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41 #end if
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42 #end if
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43
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44 #import json
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45 #import os
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46 Rscript '${__tool_directory__}/deseq2.R'
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47 --cores \${GALAXY_SLOTS:-1}
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48 -o '$deseq_out'
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49 #if $pdf:
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50 -p '$plots'
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51 #end if
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52 #if $normCounts:
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53 -n '$counts_out'
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54 #end if
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55 #if $normRLog:
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56 -r '$rlog_out'
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57 #end if
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58 #if $normVST:
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59 -v '$vst_out'
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60 #end if
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61 #set $filename_to_element_identifiers = {}
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62 #set $temp_factor_names = list()
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63 #for $factor in $select_data.rep_factorName:
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64 #set $temp_factor = list()
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65 #for $level in $factor.rep_factorLevel:
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66 #set $count_files = list()
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67 #if $select_data.how == 'group_tags':
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68 #for $group in $level.groups.value:
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69 #for $file in $select_data.countsFile.get_datasets_for_group($group):
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70 $count_files.append(str($file))
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71 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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72 #end for
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73 #end for
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74 #else:
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75 #for $file in $level.countsFile:
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76 $count_files.append(str($file))
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77 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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78 #end for
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79 #end if
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80 $temp_factor.append( {str($level.factorLevel): $count_files} )
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81 #end for
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82 $temp_factor.reverse()
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83 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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84 #end for
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85
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86 $header
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87
11
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88 -f '#echo json.dumps(temp_factor_names)#'
12
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89 -l '#echo json.dumps(filename_to_element_identifiers)#'
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90 #if $esf:
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91 -e $esf
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92 #end if
11
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93 -t $fit_type
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94 #if $batch_factors:
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95 --batch_factors '$batch_factors'
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96 #end if
11
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97 #if $outlier_replace_off:
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98 -a
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99 #end if
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100 #if $outlier_filter_off:
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101 -b
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102 #end if
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103 #if $auto_mean_filter_off:
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104 -c
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105 #end if
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106 #if $many_contrasts:
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107 -m
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108 #end if
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109 #if $tximport.tximport_selector == 'tximport':
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110 -i
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111 -y $tximport.txtype
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112 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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113 -x mapping.gff
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114 #else:
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115 -x mapping.txt
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116 #end if
5
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117
11
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118 #end if
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119 ]]></command>
0
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120 <inputs>
22
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121 <conditional name="select_data">
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122 <param name="how" type="select">
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123 <option value="datasets_per_level">Select datasets per level</option>
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124 <option value="group_tags">Select group tags corresponding to levels</option>
0
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125 </param>
22
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126 <when value="group_tags">
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127 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
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128 <expand macro="factor_repeat">
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129 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
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130 </expand>
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131 </when>
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132 <when value="datasets_per_level">
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133 <expand macro="factor_repeat">
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134 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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135 </expand>
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136 </when>
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137 </conditional>
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138
17
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139 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>
15
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140 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
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141
6
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142 <conditional name="tximport">
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143 <param name="tximport_selector" type="select" label="Choice of Input data">
14
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144 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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145 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
6
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146 </param>
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147 <when value="tximport">
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148 <param name="txtype" type="select" label="Program used to generate TPMs">
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149 <option value="kallisto">kallisto</option>
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150 <option value="sailfish">Sailfish</option>
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151 <option value="salmon">Salmon</option>
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152 </param>
6
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153 <conditional name="mapping_format">
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154 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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155 <option value="gtf" selected="True">GTF/GFF3</option>
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156 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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157 </param>
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158 <when value="gtf">
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159 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
6
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160 </when>
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161 <when value="tabular">
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162 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
6
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163 </when>
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164 </conditional>
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165 </when>
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166 <when value="count" />
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167 </conditional>
0
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168 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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169 label="Visualising the analysis results"
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170 help="output an additional PDF files" />
6
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171 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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172 label="Output normalized counts table" />
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173 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
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174 label="Output rLog normalized table" />
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175 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
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176 label="Output VST normalized table" />
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177 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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178 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
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179 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
18
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180 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
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181 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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182 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
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183 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
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184 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
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185 some zeros, by calculating a modified geometric mean by taking the n-th root of the product of the non-zero counts. This evolved out of
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186 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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187 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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188 <option value="" selected="true">No Selection (use default)</option>
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189 <option value="ratio">ratio</option>
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190 <option value="poscounts">poscounts</option>
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191 <option value="iterate">iterate</option>
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192 </param>
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193 <param name="fit_type" type="select" label="Fit type">
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194 <option value="1" selected="true">parametric</option>
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195 <option value="2">local</option>
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196 <option value="3">mean</option>
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197 </param>
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198 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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199 label="Turn off outliers replacement (only affects with >6 replicates)"
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200 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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201 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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202 or normalization factor for that sample" />
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203 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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204 label="Turn off outliers filtering (only affects with >2 replicates)"
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205 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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206 filter genes which contain a Cook’s distance above a cutoff" />
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207 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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208 label="Turn off independent filtering"
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209 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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210 </inputs>
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211 <outputs>
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212 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
0
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213 <filter>many_contrasts is False</filter>
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214 <actions>
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215 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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216 </actions>
0
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217 </data>
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218 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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219 <filter>many_contrasts is True</filter>
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220 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
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221 </collection>
19
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222 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
0
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223 <filter>pdf == True</filter>
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224 </data>
19
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225 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
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226 <filter>normCounts == True</filter>
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227 </data>
19
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228 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
18
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229 <filter>normRLog == True</filter>
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230 </data>
19
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231 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
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232 <filter>normVST == True</filter>
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233 </data>
0
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234 </outputs>
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235 <tests>
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236 <!--Ensure counts files with header works -->
18
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237 <test expect_num_outputs="4">
0
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238 <repeat name="rep_factorName">
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239 <param name="factorName" value="Treatment"/>
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240 <repeat name="rep_factorLevel">
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241 <param name="factorLevel" value="Treated"/>
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242 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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243 </repeat>
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244 <repeat name="rep_factorLevel">
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245 <param name="factorLevel" value="Untreated"/>
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246 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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247 </repeat>
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248 </repeat>
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249 <param name="pdf" value="False"/>
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250 <param name="normCounts" value="True"/>
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251 <param name="normRLog" value="True"/>
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252 <param name="normVST" value="True"/>
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253 <output name="counts_out">
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254 <assert_contents>
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255 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
15
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256 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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257 </assert_contents>
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258 </output>
18
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259 <output name="rlog_out">
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260 <assert_contents>
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261 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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262 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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263 </assert_contents>
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264 </output>
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265 <output name="vst_out">
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266 <assert_contents>
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267 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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268 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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269 </assert_contents>
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270 </output>
15
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271 <output name="deseq_out" >
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272 <assert_contents>
19
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273 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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274 </assert_contents>
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275 </output>
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276 </test>
17
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277 <!--Ensure additional batch factor correction works -->
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278 <test expect_num_outputs="2">
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279 <repeat name="rep_factorName">
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280 <param name="factorName" value="Treatment"/>
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281 <repeat name="rep_factorLevel">
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282 <param name="factorLevel" value="Treated"/>
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283 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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284 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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285 <repeat name="rep_factorLevel">
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286 <param name="factorLevel" value="Untreated"/>
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287 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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288 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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289 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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290 <param name="batch_factors" value="batch_factors.tab"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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291 <param name="pdf" value="False"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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292 <param name="normCounts" value="True"/>
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293 <output name="deseq_out">
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294 <assert_contents>
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295 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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296 </assert_contents>
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297 </output>
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298 </test>
15
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299 <!--Ensure counts files without header works -->
18
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300 <test expect_num_outputs="4">
15
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301 <repeat name="rep_factorName">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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302 <param name="factorName" value="Treatment"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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303 <repeat name="rep_factorLevel">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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304 <param name="factorLevel" value="Treated"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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305 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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306 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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307 <repeat name="rep_factorLevel">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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308 <param name="factorLevel" value="Untreated"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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309 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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310 </repeat>
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311 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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312 <param name="header" value="False"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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313 <param name="pdf" value="False"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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314 <param name="normCounts" value="True"/>
18
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315 <param name="normRLog" value="True"/>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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316 <param name="normVST" value="True"/>
15
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317 <output name="counts_out">
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318 <assert_contents>
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319 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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320 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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321 </assert_contents>
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322 </output>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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323 <output name="rlog_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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324 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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325 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
326 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
327 </assert_contents>
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diff changeset
328 </output>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
329 <output name="vst_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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330 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
331 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
332 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
333 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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334 </output>
15
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diff changeset
335 <output name="deseq_out" >
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336 <assert_contents>
19
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iuc
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337 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
15
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338 </assert_contents>
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339 </output>
6
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340 </test>
11
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341 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
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342 <test expect_num_outputs="1">
6
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343 <repeat name="rep_factorName">
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344 <param name="factorName" value="Treatment"/>
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345 <repeat name="rep_factorLevel">
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346 <param name="factorLevel" value="Treated"/>
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347 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
6
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348 </repeat>
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349 <repeat name="rep_factorLevel">
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350 <param name="factorLevel" value="Untreated"/>
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351 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
6
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352 </repeat>
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353 </repeat>
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354 <param name="pdf" value="False"/>
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355 <param name="tximport_selector" value="tximport"/>
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356 <param name="txtype" value="sailfish"/>
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357 <param name="mapping_format_selector" value="tabular"/>
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358 <param name="tabular_file" value="tx2gene.tab"/>
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359 <output name="deseq_out" >
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360 <assert_contents>
19
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361 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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362 </assert_contents>
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363 </output>
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364 </test>
20
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365 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
19
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366 <test expect_num_outputs="1">
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367 <repeat name="rep_factorName">
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368 <param name="factorName" value="Treatment"/>
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369 <repeat name="rep_factorLevel">
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370 <param name="factorLevel" value="Treated"/>
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371 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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372 </repeat>
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373 <repeat name="rep_factorLevel">
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374 <param name="factorLevel" value="Untreated"/>
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375 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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376 </repeat>
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377 </repeat>
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378 <param name="pdf" value="False"/>
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379 <param name="tximport_selector" value="tximport"/>
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380 <param name="txtype" value="sailfish"/>
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381 <param name="mapping_format_selector" value="gtf"/>
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382 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
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383 <output name="deseq_out" >
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384 <assert_contents>
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385 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
15
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386 </assert_contents>
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387 </output>
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388 </test>
20
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389 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
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390 <test expect_num_outputs="1">
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391 <repeat name="rep_factorName">
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392 <param name="factorName" value="Treatment"/>
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393 <repeat name="rep_factorLevel">
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394 <param name="factorLevel" value="Treated"/>
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395 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
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396 </repeat>
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397 <repeat name="rep_factorLevel">
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398 <param name="factorLevel" value="Untreated"/>
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399 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
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400 </repeat>
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401 </repeat>
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402 <param name="pdf" value="False"/>
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diff changeset
403 <param name="tximport_selector" value="tximport"/>
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404 <param name="txtype" value="sailfish"/>
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405 <param name="mapping_format_selector" value="gtf"/>
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diff changeset
406 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
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407 <output name="deseq_out" >
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408 <assert_contents>
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409 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
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410 </assert_contents>
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411 </output>
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412 </test>
22
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413 <!--Ensure group tags can be used to select factor levels -->
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414 <test expect_num_outputs="1">
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415 <param name="select_data|how" value="group_tags"/>
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416 <param name="select_data|countsFile">
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417 <collection type="list">
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418 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
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419 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
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420 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
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421 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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422 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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423 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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424 </collection>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
425 </param>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
426 <repeat name="rep_factorName">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
427 <param name="factorName" value="Treatment"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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428 <repeat name="rep_factorLevel">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
429 <param name="factorLevel" value="Treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
430 <param name="groups" value="primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
431 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
432 <repeat name="rep_factorLevel">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
433 <param name="factorLevel" value="Untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
434 <param name="groups" value="primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
435 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
436 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 21
diff changeset
437 <param name="pdf" value="False"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
438 <param name="tximport_selector" value="tximport"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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439 <param name="txtype" value="sailfish"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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440 <param name="mapping_format_selector" value="tabular"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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441 <param name="tabular_file" value="tx2gene.tab"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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diff changeset
442 <output name="deseq_out" >
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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443 <assert_contents>
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444 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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445 </assert_contents>
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446 </output>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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447 </test>
24
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448 <!--Ensure many_contrasts produces output collection -->
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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449 <test expect_num_outputs="1">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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450 <param name="select_data|how" value="group_tags"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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451 <param name="select_data|countsFile">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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452 <collection type="list">
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453 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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454 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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455 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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456 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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457 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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458 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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459 </collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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460 </param>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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461 <repeat name="rep_factorName">
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462 <param name="factorName" value="Treatment"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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463 <repeat name="rep_factorLevel">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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464 <param name="factorLevel" value="Treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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465 <param name="groups" value="primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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466 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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467 <repeat name="rep_factorLevel">
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468 <param name="factorLevel" value="Untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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469 <param name="groups" value="primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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470 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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471 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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472 <param name="pdf" value="False"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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473 <param name="tximport_selector" value="tximport"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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474 <param name="txtype" value="sailfish"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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475 <param name="mapping_format_selector" value="tabular"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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476 <param name="tabular_file" value="tx2gene.tab"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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477 <param name="many_contrasts" value="true"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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478 <output_collection name="split_output" type="list" count="1">
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479 <element name="Treatment_Treated_vs_Untreated">
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480 <assert_contents>
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481 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
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482 </assert_contents>
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483 </element>
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484 </output_collection>
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485 </test>
0
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486 </tests>
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487 <help><![CDATA[
0
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488 .. class:: infomark
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489
3
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490 **What it does**
0
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491
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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492 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
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493
11
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494 -----
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495
0
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496 **Inputs**
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497
11
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498 **Count Files**
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499
15
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500 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
0
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501
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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502 The following table gives some examples of factors and their levels:
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503
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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504 ========= ============== ===============
3
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505 Factor Factor level 1 Factor level 2
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506 --------- -------------- ---------------
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diff changeset
507 Treatment Treated Untreated
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
508 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
509 Condition Knockdown Wildtype
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
510 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
511 TimePoint Day4 Day1
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
512 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
513 SeqType SingleEnd PairedEnd
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
514 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
515 Gender Female Male
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
516 ========= ============== ===============
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
517
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
518 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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519
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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520 DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2.
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
521
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
522 **Salmon or Sailfish Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
523
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
524 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below.
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
525
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
526 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
527
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
528 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
529 Name Length EffectiveLength TPM NumReads
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
530 ------------ ---------- --------------- ----------- -----------
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
531 NR_001526 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
532 NR_001526_1 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
533 NR_001526_2 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
534 NM_130786 1764 1956.04 2.47415 109.165
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
535 NR_015380 2129 2139.53 1.77331 85.5821
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
536 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
537 NM_001198819 9527 7964.62 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
538 NM_001198820 9410 7855.78 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
539 NM_014576 9267 7714.88 0.0481114 8.37255
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
540 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
541
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
542 **kallisto Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
543
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
544 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
545
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
546 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
547
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
548 ============ ========== =============== =========== ===========
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
549 target_id length eff_length est_counts tpm
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
550 ------------ ---------- --------------- ----------- -----------
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
551 NR_001526 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
552 NR_001526_1 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
553 NR_001526_2 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
554 NM_130786 1764 1956.04 109.165 2.47415
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
555 NR_015380 2129 2139.53 85.5821 1.77331
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
556 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
557 NM_001198819 9527 7964.62 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
558 NM_001198820 9410 7855.78 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
559 NM_014576 9267 7714.88 8.37255 0.0481114
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
560 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
561
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
562 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
563
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
564 **Output**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
565
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
566 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
567
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
568 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
569 Column Description
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
570 ------ ----------------------------------------------------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
571 1 Gene Identifiers
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
572 2 mean normalised counts, averaged over all samples from both conditions
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
573 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
574 4 standard error estimate for the log2 fold change estimate
2
afe2a77c5900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents: 1
diff changeset
575 5 Wald statistic
afe2a77c5900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents: 1
diff changeset
576 6 p value for the statistical significance of this change
afe2a77c5900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents: 1
diff changeset
577 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
578 which controls false discovery rate (FDR)
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
579 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
580
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
581 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
582 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
583 ]]></help>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
584 <citations>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
585 <citation type="doi">10.1186/s13059-014-0550-8</citation>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
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diff changeset
586 </citations>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
587 </tool>