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annotate deseq2.xml @ 20:89d26b11d452 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
author iuc
date Thu, 06 Dec 2018 15:49:22 -0500
parents c56e0689e46e
children a6fc9228e1a0
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1 <tool id="deseq2" name="DESeq2" version="2.11.40.4">
0
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2 <description>Determines differentially expressed features from count tables</description>
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3 <requirements>
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4 <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement>
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5 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
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6 <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement>
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7 <requirement type="package" version="1.8.0">bioconductor-tximport</requirement>
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8 <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement>
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9 <requirement type="package" version="1.20.2">r-getopt</requirement>
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10 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
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11 <requirement type="package" version="3.0.1">r-gplots</requirement>
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12 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
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13 <requirement type="package" version="0.2.20">r-rjson</requirement>
0
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14 </requirements>
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15 <stdio>
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16 <regex match="Execution halted"
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17 source="both"
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18 level="fatal"
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19 description="Execution halted." />
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20 <regex match="Error in"
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21 source="both"
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22 level="fatal"
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23 description="An undefined error occurred, please check your input carefully and contact your administrator." />
0
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24 <regex match="Fatal error"
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25 source="both"
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26 level="fatal"
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27 description="An undefined error occurred, please check your input carefully and contact your administrator." />
0
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28 </stdio>
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29 <version_command><![CDATA[
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30 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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31 ]]></version_command>
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32 <command><![CDATA[
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33 #if $tximport.tximport_selector == 'tximport':
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34 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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35 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
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36 #else:
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37 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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38 #end if
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39 #end if
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40
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41 #import json
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42 #import os
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43 Rscript '${__tool_directory__}/deseq2.R'
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44 -o '$deseq_out'
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45 #if $pdf:
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46 -p '$plots'
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47 #end if
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48 #if $normCounts:
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49 -n '$counts_out'
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50 #end if
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51 #if $normRLog:
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52 -r '$rlog_out'
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53 #end if
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54 #if $normVST:
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55 -v '$vst_out'
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56 #end if
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57 #set $filename_to_element_identifiers = {}
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58 #set $temp_factor_names = list()
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59 #for $factor in $rep_factorName:
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60 #set $temp_factor = list()
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61 #for $level in $factor.rep_factorLevel:
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62 #set $count_files = list()
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63 #for $file in $level.countsFile:
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64 $count_files.append(str($file))
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65 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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66 #end for
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67 $temp_factor.append( {str($level.factorLevel): $count_files} )
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68 #end for
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69 $temp_factor.reverse()
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70 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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71 #end for
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72
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73 $header
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74
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75 -f '#echo json.dumps(temp_factor_names)#'
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76 -l '#echo json.dumps(filename_to_element_identifiers)#'
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77 #if $esf:
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78 -e $esf
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79 #end if
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80 -t $fit_type
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81 #if $batch_factors:
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82 --batch_factors '$batch_factors'
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83 #end if
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84 #if $outlier_replace_off:
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85 -a
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86 #end if
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87 #if $outlier_filter_off:
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88 -b
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89 #end if
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90 #if $auto_mean_filter_off:
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91 -c
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92 #end if
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93 #if $many_contrasts:
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94 -m
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95 #end if
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96 #if $tximport.tximport_selector == 'tximport':
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97 -i
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98 -y $tximport.txtype
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99 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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100 -x mapping.gff
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101 #else:
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102 -x mapping.txt
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103 #end if
5
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104
11
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105 #end if
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106 ]]></command>
0
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107 <inputs>
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108 <repeat name="rep_factorName" title="Factor" min="1">
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109 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
0
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110 help="Only letters, numbers and underscores will be retained in this field">
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111 <sanitizer>
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112 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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113 </sanitizer>
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114 </param>
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115 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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116 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
0
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117 help="Only letters, numbers and underscores will be retained in this field">
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118 <sanitizer>
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119 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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120 </sanitizer>
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121 </param>
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122 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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123 </repeat>
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124 </repeat>
17
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125 <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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126 <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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127
6
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128 <conditional name="tximport">
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129 <param name="tximport_selector" type="select" label="Choice of Input data">
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130 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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131 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
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132 </param>
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133 <when value="tximport">
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134 <param name="txtype" type="select" label="Program used to generate TPMs">
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135 <option value="kallisto">kallisto</option>
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136 <option value="sailfish">Sailfish</option>
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137 <option value="salmon">Salmon</option>
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138 </param>
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139 <conditional name="mapping_format">
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140 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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141 <option value="gtf" selected="True">GTF/GFF3</option>
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142 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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143 </param>
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144 <when value="gtf">
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145 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
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146 </when>
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147 <when value="tabular">
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148 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
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149 </when>
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150 </conditional>
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151 </when>
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152 <when value="count" />
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153 </conditional>
0
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154 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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155 label="Visualising the analysis results"
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156 help="output an additional PDF files" />
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157 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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158 label="Output normalized counts table" />
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159 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
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160 label="Output rLog normalized table" />
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161 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
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162 label="Output VST normalized table" />
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163 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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164 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
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165 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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166 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
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167 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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168 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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169 '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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170 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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171 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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172 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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173 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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174 <option value="" selected="true">No Selection (use default)</option>
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175 <option value="ratio">ratio</option>
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176 <option value="poscounts">poscounts</option>
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177 <option value="iterate">iterate</option>
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178 </param>
0
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179 <param name="fit_type" type="select" label="Fit type">
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180 <option value="1" selected="true">parametric</option>
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181 <option value="2">local</option>
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182 <option value="3">mean</option>
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183 </param>
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184 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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185 label="Turn off outliers replacement (only affects with >6 replicates)"
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186 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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187 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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188 or normalization factor for that sample" />
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189 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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190 label="Turn off outliers filtering (only affects with >2 replicates)"
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191 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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192 filter genes which contain a Cook’s distance above a cutoff" />
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193 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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194 label="Turn off independent filtering"
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195 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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196 </inputs>
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197 <outputs>
19
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198 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
0
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199 <filter>many_contrasts is False</filter>
6
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200 <actions>
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201 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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202 </actions>
0
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203 </data>
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204 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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205 <filter>many_contrasts is True</filter>
3
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206 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
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207 </collection>
19
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208 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
0
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209 <filter>pdf == True</filter>
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210 </data>
19
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211 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
6
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212 <filter>normCounts == True</filter>
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213 </data>
19
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214 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
18
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215 <filter>normRLog == True</filter>
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216 </data>
19
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217 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
18
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218 <filter>normVST == True</filter>
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219 </data>
0
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220 </outputs>
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221 <tests>
15
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222 <!--Ensure counts files with header works -->
18
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223 <test expect_num_outputs="4">
0
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224 <repeat name="rep_factorName">
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225 <param name="factorName" value="Treatment"/>
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226 <repeat name="rep_factorLevel">
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227 <param name="factorLevel" value="Treated"/>
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228 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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229 </repeat>
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230 <repeat name="rep_factorLevel">
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231 <param name="factorLevel" value="Untreated"/>
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232 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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233 </repeat>
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234 </repeat>
6
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235 <param name="pdf" value="False"/>
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236 <param name="normCounts" value="True"/>
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237 <param name="normRLog" value="True"/>
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238 <param name="normVST" value="True"/>
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239 <output name="counts_out">
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240 <assert_contents>
16
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241 <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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242 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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243 </assert_contents>
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244 </output>
18
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245 <output name="rlog_out">
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246 <assert_contents>
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247 <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" />
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248 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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249 </assert_contents>
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250 </output>
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251 <output name="vst_out">
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252 <assert_contents>
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253 <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" />
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254 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
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255 </assert_contents>
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256 </output>
15
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257 <output name="deseq_out" >
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258 <assert_contents>
19
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259 <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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260 </assert_contents>
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261 </output>
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262 </test>
17
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263 <!--Ensure additional batch factor correction works -->
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264 <test expect_num_outputs="2">
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265 <repeat name="rep_factorName">
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266 <param name="factorName" value="Treatment"/>
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267 <repeat name="rep_factorLevel">
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268 <param name="factorLevel" value="Treated"/>
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269 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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270 </repeat>
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271 <repeat name="rep_factorLevel">
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272 <param name="factorLevel" value="Untreated"/>
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273 <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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274 </repeat>
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275 </repeat>
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276 <param name="batch_factors" value="batch_factors.tab"/>
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277 <param name="pdf" value="False"/>
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278 <param name="normCounts" value="True"/>
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279 <output name="deseq_out">
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280 <assert_contents>
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281 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
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282 </assert_contents>
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283 </output>
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284 </test>
15
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285 <!--Ensure counts files without header works -->
18
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286 <test expect_num_outputs="4">
15
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287 <repeat name="rep_factorName">
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288 <param name="factorName" value="Treatment"/>
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289 <repeat name="rep_factorLevel">
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290 <param name="factorLevel" value="Treated"/>
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291 <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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292 </repeat>
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293 <repeat name="rep_factorLevel">
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294 <param name="factorLevel" value="Untreated"/>
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295 <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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296 </repeat>
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297 </repeat>
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298 <param name="header" value="False"/>
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299 <param name="pdf" value="False"/>
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300 <param name="normCounts" value="True"/>
18
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301 <param name="normRLog" value="True"/>
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302 <param name="normVST" value="True"/>
15
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303 <output name="counts_out">
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304 <assert_contents>
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305 <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
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306 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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307 </assert_contents>
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308 </output>
18
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309 <output name="rlog_out">
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310 <assert_contents>
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311 <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
312 <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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313 </assert_contents>
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314 </output>
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315 <output name="vst_out">
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316 <assert_contents>
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317 <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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318 <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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319 </assert_contents>
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320 </output>
15
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diff changeset
321 <output name="deseq_out" >
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322 <assert_contents>
19
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parents: 18
diff changeset
323 <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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324 </assert_contents>
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325 </output>
6
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326 </test>
11
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327 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
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328 <test expect_num_outputs="1">
6
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329 <repeat name="rep_factorName">
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iuc
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diff changeset
330 <param name="factorName" value="Treatment"/>
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331 <repeat name="rep_factorLevel">
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332 <param name="factorLevel" value="Treated"/>
11
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333 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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diff changeset
334 </repeat>
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iuc
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diff changeset
335 <repeat name="rep_factorLevel">
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336 <param name="factorLevel" value="Untreated"/>
11
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337 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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338 </repeat>
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339 </repeat>
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340 <param name="pdf" value="False"/>
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341 <param name="tximport_selector" value="tximport"/>
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342 <param name="txtype" value="sailfish"/>
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343 <param name="mapping_format_selector" value="tabular"/>
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344 <param name="tabular_file" value="tx2gene.tab"/>
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345 <output name="deseq_out" >
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346 <assert_contents>
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347 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
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348 </assert_contents>
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349 </output>
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350 </test>
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351 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
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352 <test expect_num_outputs="1">
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353 <repeat name="rep_factorName">
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354 <param name="factorName" value="Treatment"/>
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355 <repeat name="rep_factorLevel">
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356 <param name="factorLevel" value="Treated"/>
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357 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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358 </repeat>
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359 <repeat name="rep_factorLevel">
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360 <param name="factorLevel" value="Untreated"/>
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361 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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362 </repeat>
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363 </repeat>
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364 <param name="pdf" value="False"/>
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365 <param name="tximport_selector" value="tximport"/>
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366 <param name="txtype" value="sailfish"/>
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367 <param name="mapping_format_selector" value="gtf"/>
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368 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
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369 <output name="deseq_out" >
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370 <assert_contents>
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371 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
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372 </assert_contents>
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373 </output>
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374 </test>
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375 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
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376 <test expect_num_outputs="1">
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377 <repeat name="rep_factorName">
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378 <param name="factorName" value="Treatment"/>
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379 <repeat name="rep_factorLevel">
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380 <param name="factorLevel" value="Treated"/>
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381 <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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382 </repeat>
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383 <repeat name="rep_factorLevel">
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384 <param name="factorLevel" value="Untreated"/>
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385 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
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386 </repeat>
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387 </repeat>
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388 <param name="pdf" value="False"/>
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389 <param name="tximport_selector" value="tximport"/>
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390 <param name="txtype" value="sailfish"/>
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391 <param name="mapping_format_selector" value="gtf"/>
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392 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
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393 <output name="deseq_out" >
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394 <assert_contents>
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395 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
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396 </assert_contents>
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397 </output>
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398 </test>
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399 </tests>
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400 <help><![CDATA[
0
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401 .. class:: infomark
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402
3
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403 **What it does**
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404
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405 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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406
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407 -----
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408
0
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409 **Inputs**
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410
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411 **Count Files**
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412
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413 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.
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414
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415 The following table gives some examples of factors and their levels:
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416
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417 ========= ============== ===============
3
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418 Factor Factor level 1 Factor level 2
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419 --------- -------------- ---------------
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420 Treatment Treated Untreated
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421 --------- -------------- ---------------
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422 Condition Knockdown Wildtype
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423 --------- -------------- ---------------
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424 TimePoint Day4 Day1
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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425 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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426 SeqType SingleEnd PairedEnd
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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427 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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428 Gender Female Male
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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429 ========= ============== ===============
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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430
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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431 *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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432
15
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433 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
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434
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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435 **Salmon or Sailfish Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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436
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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437 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
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438
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439 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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440
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441 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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442 Name Length EffectiveLength TPM NumReads
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443 ------------ ---------- --------------- ----------- -----------
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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444 NR_001526 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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445 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
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446 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
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447 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
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448 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
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449 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
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450 NM_001198819 9527 7964.62 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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451 NM_001198820 9410 7855.78 0 0
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452 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
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453 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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454
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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455 **kallisto Files**
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456
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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457 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
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458
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459 Example:
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460
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461 ============ ========== =============== =========== ===========
15
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462 target_id length eff_length est_counts tpm
11
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463 ------------ ---------- --------------- ----------- -----------
15
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464 NR_001526 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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465 NR_001526_1 164 20.4518 0 0
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466 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
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467 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
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468 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
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469 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
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470 NM_001198819 9527 7964.62 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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471 NM_001198820 9410 7855.78 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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472 NM_014576 9267 7714.88 8.37255 0.0481114
11
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473 ============ ========== =============== =========== ===========
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474
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475 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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476
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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477 **Output**
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478
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479 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
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480
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481 ====== ==========================================================
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482 Column Description
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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483 ------ ----------------------------------------------------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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484 1 Gene Identifiers
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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485 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
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486 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
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487 4 standard error estimate for the log2 fold change estimate
2
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488 5 Wald statistic
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489 6 p value for the statistical significance of this change
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490 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
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491 which controls false discovery rate (FDR)
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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492 ====== ==========================================================
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493
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494 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
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495 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
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496 ]]></help>
0
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497 <citations>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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498 <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
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499 </citations>
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500 </tool>