Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 33:4f497a8a72e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3
author iuc
date Mon, 28 Jan 2019 12:03:36 -0500
parents 13f324f9cdb7
children f98981133ec0
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1 <tool id="deseq2" name="DESeq2" version="2.11.40.5">
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>
6
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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." />
6
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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." />
6
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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 --cores \${GALAXY_SLOTS:-1}
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45 -o '$deseq_out'
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46 #if $pdf:
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47 -p '$plots'
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48 #end if
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49 #if $normCounts:
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50 -n '$counts_out'
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51 #end if
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52 #if $normRLog:
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53 -r '$rlog_out'
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54 #end if
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55 #if $normVST:
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56 -v '$vst_out'
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57 #end if
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58 #set $filename_to_element_identifiers = {}
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59 #set $temp_factor_names = list()
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60 #for $factor in $rep_factorName:
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61 #set $temp_factor = list()
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62 #for $level in $factor.rep_factorLevel:
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63 #set $count_files = list()
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64 #for $file in $level.countsFile:
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65 $count_files.append(str($file))
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66 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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67 #end for
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68 $temp_factor.append( {str($level.factorLevel): $count_files} )
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69 #end for
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70 $temp_factor.reverse()
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71 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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72 #end for
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73
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74 $header
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75
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76 -f '#echo json.dumps(temp_factor_names)#'
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77 -l '#echo json.dumps(filename_to_element_identifiers)#'
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78 #if $esf:
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79 -e $esf
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80 #end if
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81 -t $fit_type
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82 #if $batch_factors:
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83 --batch_factors '$batch_factors'
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84 #end if
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85 #if $outlier_replace_off:
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86 -a
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87 #end if
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88 #if $outlier_filter_off:
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89 -b
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90 #end if
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91 #if $auto_mean_filter_off:
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92 -c
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93 #end if
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94 #if $many_contrasts:
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95 -m
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96 #end if
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97 #if $tximport.tximport_selector == 'tximport':
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98 -i
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99 -y $tximport.txtype
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100 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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101 -x mapping.gff
23
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102 #else:
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103 -x mapping.txt
17
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104 #end if
16
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105
23
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106 #end if
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107 ]]></command>
0
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108 <inputs>
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109 <repeat name="rep_factorName" title="Factor" min="1">
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110 <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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111 help="Only letters, numbers and underscores will be retained in this field">
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112 <sanitizer>
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113 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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114 </sanitizer>
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115 </param>
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116 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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117 <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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118 help="Only letters, numbers and underscores will be retained in this field">
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119 <sanitizer>
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120 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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121 </sanitizer>
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122 </param>
6
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123 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
0
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124 </repeat>
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125 </repeat>
29
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126 <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."/>
27
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127 <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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128
17
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129 <conditional name="tximport">
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130 <param name="tximport_selector" type="select" label="Choice of Input data">
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131 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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132 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
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133 </param>
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134 <when value="tximport">
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135 <param name="txtype" type="select" label="Program used to generate TPMs">
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136 <option value="kallisto">kallisto</option>
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137 <option value="sailfish">Sailfish</option>
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138 <option value="salmon">Salmon</option>
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139 </param>
17
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140 <conditional name="mapping_format">
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141 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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142 <option value="gtf" selected="True">GTF/GFF3</option>
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143 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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144 </param>
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145 <when value="gtf">
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146 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
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147 </when>
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148 <when value="tabular">
31
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149 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
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150 </when>
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151 </conditional>
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152 </when>
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153 <when value="count" />
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154 </conditional>
0
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155 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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156 label="Visualising the analysis results"
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157 help="output an additional PDF files" />
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158 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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159 label="Output normalized counts table" />
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160 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
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161 label="Output rLog normalized table" />
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162 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
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163 label="Output VST normalized table" />
0
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164 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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165 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
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166 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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167 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
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168 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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169 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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170 '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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171 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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172 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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173 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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174 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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175 <option value="" selected="true">No Selection (use default)</option>
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176 <option value="ratio">ratio</option>
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177 <option value="poscounts">poscounts</option>
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178 <option value="iterate">iterate</option>
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179 </param>
0
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180 <param name="fit_type" type="select" label="Fit type">
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181 <option value="1" selected="true">parametric</option>
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182 <option value="2">local</option>
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183 <option value="3">mean</option>
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184 </param>
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185 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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186 label="Turn off outliers replacement (only affects with >6 replicates)"
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187 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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188 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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189 or normalization factor for that sample" />
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190 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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191 label="Turn off outliers filtering (only affects with >2 replicates)"
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192 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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193 filter genes which contain a Cook’s distance above a cutoff" />
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194 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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195 label="Turn off independent filtering"
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196 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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197 </inputs>
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198 <outputs>
31
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199 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
0
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200 <filter>many_contrasts is False</filter>
17
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201 <actions>
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202 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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203 </actions>
0
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204 </data>
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205 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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206 <filter>many_contrasts is True</filter>
15
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207 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
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208 </collection>
31
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209 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
0
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210 <filter>pdf == True</filter>
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211 </data>
31
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212 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
17
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213 <filter>normCounts == True</filter>
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214 </data>
31
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215 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
30
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216 <filter>normRLog == True</filter>
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217 </data>
31
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218 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
30
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219 <filter>normVST == True</filter>
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220 </data>
0
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221 </outputs>
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222 <tests>
27
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223 <!--Ensure counts files with header works -->
30
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224 <test expect_num_outputs="4">
0
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225 <repeat name="rep_factorName">
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226 <param name="factorName" value="Treatment"/>
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227 <repeat name="rep_factorLevel">
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228 <param name="factorLevel" value="Treated"/>
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229 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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230 </repeat>
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231 <repeat name="rep_factorLevel">
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232 <param name="factorLevel" value="Untreated"/>
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233 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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234 </repeat>
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235 </repeat>
17
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236 <param name="pdf" value="False"/>
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237 <param name="normCounts" value="True"/>
30
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238 <param name="normRLog" value="True"/>
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239 <param name="normVST" value="True"/>
27
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240 <output name="counts_out">
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241 <assert_contents>
28
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242 <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" />
27
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243 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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244 </assert_contents>
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245 </output>
30
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246 <output name="rlog_out">
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247 <assert_contents>
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248 <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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249 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
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250 </assert_contents>
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251 </output>
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252 <output name="vst_out">
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253 <assert_contents>
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254 <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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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255 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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256 </assert_contents>
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257 </output>
27
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258 <output name="deseq_out" >
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259 <assert_contents>
31
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260 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
27
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261 </assert_contents>
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262 </output>
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263 </test>
29
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264 <!--Ensure additional batch factor correction works -->
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265 <test expect_num_outputs="2">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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266 <repeat name="rep_factorName">
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267 <param name="factorName" value="Treatment"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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268 <repeat name="rep_factorLevel">
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269 <param name="factorLevel" value="Treated"/>
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270 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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271 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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272 <repeat name="rep_factorLevel">
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273 <param name="factorLevel" value="Untreated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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274 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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275 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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276 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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277 <param name="batch_factors" value="batch_factors.tab"/>
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278 <param name="pdf" value="False"/>
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279 <param name="normCounts" value="True"/>
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280 <output name="deseq_out">
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281 <assert_contents>
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282 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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283 </assert_contents>
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284 </output>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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285 </test>
27
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286 <!--Ensure counts files without header works -->
30
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287 <test expect_num_outputs="4">
27
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288 <repeat name="rep_factorName">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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289 <param name="factorName" value="Treatment"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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290 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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291 <param name="factorLevel" value="Treated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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292 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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293 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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294 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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295 <param name="factorLevel" value="Untreated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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296 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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297 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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298 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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299 <param name="header" value="False"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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300 <param name="pdf" value="False"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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301 <param name="normCounts" value="True"/>
30
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diff changeset
302 <param name="normRLog" value="True"/>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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303 <param name="normVST" value="True"/>
27
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304 <output name="counts_out">
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305 <assert_contents>
dc6bc19f05ab 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="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" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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307 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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308 </assert_contents>
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309 </output>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
310 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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311 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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312 <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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
313 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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314 </assert_contents>
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315 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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316 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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317 <assert_contents>
3b9af9a27b5b 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="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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
319 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
320 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
321 </output>
27
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diff changeset
322 <output name="deseq_out" >
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323 <assert_contents>
31
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324 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
325 </assert_contents>
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326 </output>
17
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327 </test>
23
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diff changeset
328 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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329 <test expect_num_outputs="1">
17
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diff changeset
330 <repeat name="rep_factorName">
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diff changeset
331 <param name="factorName" value="Treatment"/>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
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diff changeset
332 <repeat name="rep_factorLevel">
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diff changeset
333 <param name="factorLevel" value="Treated"/>
23
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diff changeset
334 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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335 </repeat>
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336 <repeat name="rep_factorLevel">
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337 <param name="factorLevel" value="Untreated"/>
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338 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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339 </repeat>
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340 </repeat>
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341 <param name="pdf" value="False"/>
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342 <param name="tximport_selector" value="tximport"/>
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343 <param name="txtype" value="sailfish"/>
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344 <param name="mapping_format_selector" value="tabular"/>
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345 <param name="tabular_file" value="tx2gene.tab"/>
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346 <output name="deseq_out" >
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347 <assert_contents>
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348 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
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349 </assert_contents>
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350 </output>
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351 </test>
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352 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
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353 <test expect_num_outputs="1">
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354 <repeat name="rep_factorName">
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355 <param name="factorName" value="Treatment"/>
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356 <repeat name="rep_factorLevel">
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357 <param name="factorLevel" value="Treated"/>
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358 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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359 </repeat>
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360 <repeat name="rep_factorLevel">
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361 <param name="factorLevel" value="Untreated"/>
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362 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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363 </repeat>
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364 </repeat>
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365 <param name="pdf" value="False"/>
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366 <param name="tximport_selector" value="tximport"/>
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367 <param name="txtype" value="sailfish"/>
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368 <param name="mapping_format_selector" value="gtf"/>
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369 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
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370 <output name="deseq_out" >
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371 <assert_contents>
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372 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
27
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373 </assert_contents>
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374 </output>
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375 </test>
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376 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
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377 <test expect_num_outputs="1">
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378 <repeat name="rep_factorName">
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379 <param name="factorName" value="Treatment"/>
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380 <repeat name="rep_factorLevel">
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381 <param name="factorLevel" value="Treated"/>
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382 <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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383 </repeat>
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384 <repeat name="rep_factorLevel">
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385 <param name="factorLevel" value="Untreated"/>
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386 <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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387 </repeat>
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388 </repeat>
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389 <param name="pdf" value="False"/>
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390 <param name="tximport_selector" value="tximport"/>
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391 <param name="txtype" value="sailfish"/>
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392 <param name="mapping_format_selector" value="gtf"/>
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393 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
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394 <output name="deseq_out" >
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395 <assert_contents>
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396 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
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397 </assert_contents>
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398 </output>
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399 </test>
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400 </tests>
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401 <help><![CDATA[
0
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402 .. class:: infomark
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403
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404 **What it does**
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405
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406 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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407
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408 -----
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409
0
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410 **Inputs**
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411
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412 **Count Files**
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413
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414 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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415
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416 The following table gives some examples of factors and their levels:
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417
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418 ========= ============== ===============
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419 Factor Factor level 1 Factor level 2
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420 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
421 Treatment Treated Untreated
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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422 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
423 Condition Knockdown Wildtype
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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424 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
425 TimePoint Day4 Day1
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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426 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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427 SeqType SingleEnd PairedEnd
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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428 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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429 Gender Female Male
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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430 ========= ============== ===============
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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431
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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432 *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.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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433
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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434 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.
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
435
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
436 **Salmon or Sailfish Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
437
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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438 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.
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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439
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
440 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
441
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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442 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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443 Name Length EffectiveLength TPM NumReads
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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444 ------------ ---------- --------------- ----------- -----------
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
445 NR_001526 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
446 NR_001526_1 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
447 NR_001526_2 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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448 NM_130786 1764 1956.04 2.47415 109.165
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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449 NR_015380 2129 2139.53 1.77331 85.5821
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
450 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
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451 NM_001198819 9527 7964.62 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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452 NM_001198820 9410 7855.78 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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453 NM_014576 9267 7714.88 0.0481114 8.37255
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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454 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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parents: 22
diff changeset
455
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
456 **kallisto Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
457
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
458 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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459
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
460 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
461
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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462 ============ ========== =============== =========== ===========
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
463 target_id length eff_length est_counts tpm
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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464 ------------ ---------- --------------- ----------- -----------
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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465 NR_001526 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
466 NR_001526_1 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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467 NR_001526_2 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
468 NM_130786 1764 1956.04 109.165 2.47415
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
469 NR_015380 2129 2139.53 85.5821 1.77331
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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470 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
471 NM_001198819 9527 7964.62 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
472 NM_001198820 9410 7855.78 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
473 NM_014576 9267 7714.88 8.37255 0.0481114
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
474 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
475
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
476 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
477
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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478 **Output**
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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479
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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480 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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481
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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482 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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483 Column Description
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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484 ------ ----------------------------------------------------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
485 1 Gene Identifiers
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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486 2 mean normalised counts, averaged over all samples from both conditions
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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487 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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488 4 standard error estimate for the log2 fold change estimate
13
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489 5 Wald statistic
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
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490 6 p value for the statistical significance of this change
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
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491 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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492 which controls false discovery rate (FDR)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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493 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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494
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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495 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
23
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496 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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497 ]]></help>
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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498 <citations>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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499 <citation type="doi">10.1186/s13059-014-0550-8</citation>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
500 </citations>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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501 </tool>