Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 38:cf2c5e8ea088 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
author iuc
date Fri, 08 Jan 2021 20:29:23 +0000
parents 951876579237
children b30a443484ab
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1 <tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">
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2 <description>Determines differentially expressed features from count tables</description>
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3 <macros>
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4 <import>deseq2_macros.xml</import>
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5 </macros>
0
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6 <requirements>
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7 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
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8 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
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9 <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
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10 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
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11 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
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12 <requirement type="package" version="1.20.2">r-getopt</requirement>
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13 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
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14 <requirement type="package" version="3.0.1">r-gplots</requirement>
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15 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
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16 <requirement type="package" version="0.2.20">r-rjson</requirement>
0
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17 </requirements>
6
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18 <stdio>
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19 <regex match="Execution halted"
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20 source="both"
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21 level="fatal"
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22 description="Execution halted." />
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23 <regex match="Error in"
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24 source="both"
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25 level="fatal"
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26 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6
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27 <regex match="Fatal error"
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28 source="both"
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29 level="fatal"
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30 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6
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31 </stdio>
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32 <version_command><![CDATA[
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33 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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34 ]]></version_command>
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35 <command><![CDATA[
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36 #if $tximport.tximport_selector == 'tximport':
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37 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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38 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
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39 #else:
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40 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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41 #end if
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42 #end if
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43
38
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44 ## This is needed for Pulsar to transfer the file
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45 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&
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46
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47 #import json
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48 #import os
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49 Rscript '${__tool_directory__}/deseq2.R'
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50 --cores \${GALAXY_SLOTS:-1}
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51 -o '$deseq_out'
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52 #if $pdf:
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53 -p '$plots'
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54 #end if
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55 #if $normCounts:
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56 -n '$counts_out'
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57 #end if
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58 #if $normRLog:
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59 -r '$rlog_out'
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60 #end if
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61 #if $normVST:
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62 -v '$vst_out'
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63 #end if
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64 #set $filename_to_element_identifiers = {}
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65 #set $temp_factor_names = list()
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66 #for $factor in $select_data.rep_factorName:
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67 #set $temp_factor = list()
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68 #for $level in $factor.rep_factorLevel:
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69 #set $count_files = list()
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70 #if $select_data.how == 'group_tags':
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71 #for $group in $level.groups.value:
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72 #for $file in $select_data.countsFile.get_datasets_for_group($group):
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73 $count_files.append(str($file))
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74 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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75 #end for
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76 #end for
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77 #else:
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78 #for $file in $level.countsFile:
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79 $count_files.append(str($file))
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80 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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81 #end for
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82 #end if
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83 $temp_factor.append( {str($level.factorLevel): $count_files} )
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84 #end for
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85 $temp_factor.reverse()
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86 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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87 #end for
27
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88
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89 $header
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90
23
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91 -f '#echo json.dumps(temp_factor_names)#'
24
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92 -l '#echo json.dumps(filename_to_element_identifiers)#'
30
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93 #if $esf:
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94 -e $esf
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95 #end if
23
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96 -t $fit_type
30
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97 #if $batch_factors:
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98 --batch_factors '$batch_factors'
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99 #end if
23
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100 #if $outlier_replace_off:
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101 -a
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102 #end if
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103 #if $outlier_filter_off:
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104 -b
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105 #end if
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106 #if $auto_mean_filter_off:
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107 -c
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108 #end if
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109 #if $many_contrasts:
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110 -m
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111 #end if
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112 #if $tximport.tximport_selector == 'tximport':
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113 -i
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114 -y $tximport.txtype
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115 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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116 -x mapping.gff
23
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117 #else:
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118 -x mapping.txt
17
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119 #end if
16
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120
23
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121 #end if
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122 ]]></command>
0
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123 <inputs>
34
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124 <conditional name="select_data">
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125 <param name="how" type="select">
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126 <option value="datasets_per_level">Select datasets per level</option>
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127 <option value="group_tags">Select group tags corresponding to levels</option>
0
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128 </param>
34
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129 <when value="group_tags">
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130 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
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131 <expand macro="factor_repeat">
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132 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
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133 </expand>
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134 </when>
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135 <when value="datasets_per_level">
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diff changeset
136 <expand macro="factor_repeat">
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137 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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138 </expand>
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139 </when>
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140 </conditional>
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141
29
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142 <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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143 <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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144
17
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145 <conditional name="tximport">
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146 <param name="tximport_selector" type="select" label="Choice of Input data">
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147 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
23
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148 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
17
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149 </param>
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150 <when value="tximport">
23
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151 <param name="txtype" type="select" label="Program used to generate TPMs">
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152 <option value="kallisto">kallisto</option>
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153 <option value="sailfish">Sailfish</option>
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154 <option value="salmon">Salmon</option>
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155 </param>
17
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156 <conditional name="mapping_format">
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157 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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158 <option value="gtf" selected="True">GTF/GFF3</option>
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159 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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160 </param>
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161 <when value="gtf">
31
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162 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
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163 </when>
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164 <when value="tabular">
31
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165 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
17
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166 </when>
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167 </conditional>
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168 </when>
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169 <when value="count" />
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170 </conditional>
0
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171 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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172 label="Visualising the analysis results"
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173 help="output an additional PDF files" />
17
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174 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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175 label="Output normalized counts table" />
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176 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
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177 label="Output rLog normalized table" />
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178 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
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179 label="Output VST normalized table" />
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180 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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181 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
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182 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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183 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
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184 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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185 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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186 '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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187 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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188 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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189 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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190 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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191 <option value="" selected="true">No Selection (use default)</option>
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192 <option value="ratio">ratio</option>
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193 <option value="poscounts">poscounts</option>
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194 <option value="iterate">iterate</option>
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195 </param>
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196 <param name="fit_type" type="select" label="Fit type">
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197 <option value="1" selected="true">parametric</option>
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198 <option value="2">local</option>
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199 <option value="3">mean</option>
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200 </param>
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201 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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202 label="Turn off outliers replacement (only affects with >6 replicates)"
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203 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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204 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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205 or normalization factor for that sample" />
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206 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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207 label="Turn off outliers filtering (only affects with >2 replicates)"
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208 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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209 filter genes which contain a Cook’s distance above a cutoff" />
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210 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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211 label="Turn off independent filtering"
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212 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
0
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213 </inputs>
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214 <outputs>
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215 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
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216 <filter>many_contrasts is False</filter>
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217 <actions>
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218 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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219 </actions>
0
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220 </data>
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221 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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222 <filter>many_contrasts is True</filter>
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223 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
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224 </collection>
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225 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
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226 <filter>pdf == True</filter>
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227 </data>
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228 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
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229 <filter>normCounts == True</filter>
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230 </data>
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231 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
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232 <filter>normRLog == True</filter>
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233 </data>
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234 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
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235 <filter>normVST == True</filter>
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236 </data>
0
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237 </outputs>
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238 <tests>
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239 <!--Ensure counts files with header works -->
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240 <test expect_num_outputs="4">
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241 <repeat name="rep_factorName">
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242 <param name="factorName" value="Treatment"/>
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243 <repeat name="rep_factorLevel">
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244 <param name="factorLevel" value="Treated"/>
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245 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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246 </repeat>
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247 <repeat name="rep_factorLevel">
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248 <param name="factorLevel" value="Untreated"/>
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249 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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250 </repeat>
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251 </repeat>
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252 <param name="pdf" value="False"/>
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253 <param name="normCounts" value="True"/>
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254 <param name="normRLog" value="True"/>
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255 <param name="normVST" value="True"/>
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256 <output name="counts_out">
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257 <assert_contents>
28
5707d3c668d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b
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258 <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
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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259 <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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260 </assert_contents>
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261 </output>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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262 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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263 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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264 <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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diff changeset
265 <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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266 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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267 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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268 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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269 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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270 <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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271 <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
iuc
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272 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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273 </output>
27
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274 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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275 <assert_contents>
31
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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276 <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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277 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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278 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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279 </test>
29
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280 <!--Ensure additional batch factor correction works -->
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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281 <test expect_num_outputs="2">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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282 <repeat name="rep_factorName">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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283 <param name="factorName" value="Treatment"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
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284 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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285 <param name="factorLevel" value="Treated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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286 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
287 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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288 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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289 <param name="factorLevel" value="Untreated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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290 <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
iuc
parents: 28
diff changeset
291 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
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292 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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293 <param name="batch_factors" value="batch_factors.tab"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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294 <param name="pdf" value="False"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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295 <param name="normCounts" value="True"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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296 <output name="deseq_out">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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297 <assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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298 <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
iuc
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299 </assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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300 </output>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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301 </test>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
302 <!--Ensure counts files without header works -->
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
303 <test expect_num_outputs="4">
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
304 <repeat name="rep_factorName">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
305 <param name="factorName" value="Treatment"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
306 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
307 <param name="factorLevel" value="Treated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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308 <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
iuc
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diff changeset
309 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
310 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
311 <param name="factorLevel" value="Untreated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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312 <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
iuc
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diff changeset
313 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
314 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
315 <param name="header" value="False"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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316 <param name="pdf" value="False"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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317 <param name="normCounts" value="True"/>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
318 <param name="normRLog" value="True"/>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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319 <param name="normVST" value="True"/>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
320 <output name="counts_out">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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321 <assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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322 <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
iuc
parents: 26
diff changeset
323 <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
iuc
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diff changeset
324 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
325 </output>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
326 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
327 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
328 <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
iuc
parents: 29
diff changeset
329 <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
iuc
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diff changeset
330 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
331 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
332 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
333 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
334 <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
iuc
parents: 29
diff changeset
335 <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
iuc
parents: 29
diff changeset
336 </assert_contents>
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337 </output>
27
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338 <output name="deseq_out" >
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339 <assert_contents>
31
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340 <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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341 </assert_contents>
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342 </output>
17
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343 </test>
23
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344 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
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345 <test expect_num_outputs="1">
17
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346 <repeat name="rep_factorName">
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347 <param name="factorName" value="Treatment"/>
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348 <repeat name="rep_factorLevel">
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349 <param name="factorLevel" value="Treated"/>
23
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350 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
17
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351 </repeat>
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352 <repeat name="rep_factorLevel">
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353 <param name="factorLevel" value="Untreated"/>
23
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354 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
17
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355 </repeat>
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356 </repeat>
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357 <param name="pdf" value="False"/>
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358 <param name="tximport_selector" value="tximport"/>
23
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359 <param name="txtype" value="sailfish"/>
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360 <param name="mapping_format_selector" value="tabular"/>
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361 <param name="tabular_file" value="tx2gene.tab"/>
27
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362 <output name="deseq_out" >
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363 <assert_contents>
31
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364 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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365 </assert_contents>
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366 </output>
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367 </test>
32
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368 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
31
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369 <test expect_num_outputs="1">
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370 <repeat name="rep_factorName">
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371 <param name="factorName" value="Treatment"/>
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372 <repeat name="rep_factorLevel">
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373 <param name="factorLevel" value="Treated"/>
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374 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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375 </repeat>
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376 <repeat name="rep_factorLevel">
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377 <param name="factorLevel" value="Untreated"/>
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378 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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379 </repeat>
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380 </repeat>
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381 <param name="pdf" value="False"/>
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382 <param name="tximport_selector" value="tximport"/>
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383 <param name="txtype" value="sailfish"/>
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384 <param name="mapping_format_selector" value="gtf"/>
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385 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
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386 <output name="deseq_out" >
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387 <assert_contents>
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388 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
27
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389 </assert_contents>
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390 </output>
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391 </test>
32
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392 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
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393 <test expect_num_outputs="1">
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394 <repeat name="rep_factorName">
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395 <param name="factorName" value="Treatment"/>
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396 <repeat name="rep_factorLevel">
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397 <param name="factorLevel" value="Treated"/>
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398 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
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399 </repeat>
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400 <repeat name="rep_factorLevel">
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401 <param name="factorLevel" value="Untreated"/>
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402 <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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403 </repeat>
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404 </repeat>
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405 <param name="pdf" value="False"/>
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diff changeset
406 <param name="tximport_selector" value="tximport"/>
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407 <param name="txtype" value="sailfish"/>
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408 <param name="mapping_format_selector" value="gtf"/>
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diff changeset
409 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
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410 <output name="deseq_out" >
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411 <assert_contents>
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412 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
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413 </assert_contents>
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414 </output>
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415 </test>
34
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416 <!--Ensure group tags can be used to select factor levels -->
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417 <test expect_num_outputs="1">
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418 <param name="select_data|how" value="group_tags"/>
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419 <param name="select_data|countsFile">
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420 <collection type="list">
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421 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
422 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
423 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
424 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
425 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
426 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 33
diff changeset
427 </collection>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
428 </param>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 33
diff changeset
429 <repeat name="rep_factorName">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
430 <param name="factorName" value="Treatment"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 33
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431 <repeat name="rep_factorLevel">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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432 <param name="factorLevel" value="Treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
433 <param name="groups" value="primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
434 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
435 <repeat name="rep_factorLevel">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
436 <param name="factorLevel" value="Untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
437 <param name="groups" value="primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
438 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
439 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 33
diff changeset
440 <param name="pdf" value="False"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 33
diff changeset
441 <param name="tximport_selector" value="tximport"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
442 <param name="txtype" value="sailfish"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
443 <param name="mapping_format_selector" value="tabular"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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diff changeset
444 <param name="tabular_file" value="tx2gene.tab"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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diff changeset
445 <output name="deseq_out" >
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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446 <assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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447 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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448 </assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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449 </output>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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450 </test>
36
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451 <!--Ensure many_contrasts produces output collection -->
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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452 <test expect_num_outputs="1">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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453 <param name="select_data|how" value="group_tags"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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454 <param name="select_data|countsFile">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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455 <collection type="list">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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456 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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457 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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458 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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459 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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460 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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461 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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462 </collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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463 </param>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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464 <repeat name="rep_factorName">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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465 <param name="factorName" value="Treatment"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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466 <repeat name="rep_factorLevel">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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467 <param name="factorLevel" value="Treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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468 <param name="groups" value="primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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469 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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470 <repeat name="rep_factorLevel">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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471 <param name="factorLevel" value="Untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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472 <param name="groups" value="primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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473 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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474 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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475 <param name="pdf" value="False"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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476 <param name="tximport_selector" value="tximport"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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477 <param name="txtype" value="sailfish"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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diff changeset
478 <param name="mapping_format_selector" value="tabular"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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479 <param name="tabular_file" value="tx2gene.tab"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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480 <param name="many_contrasts" value="true"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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481 <output_collection name="split_output" type="list" count="1">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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482 <element name="Treatment_Treated_vs_Untreated">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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483 <assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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484 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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485 </assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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486 </element>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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487 </output_collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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488 </test>
0
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489 </tests>
23
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490 <help><![CDATA[
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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491 .. class:: infomark
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492
15
d856341e03c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1
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493 **What it does**
0
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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 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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496
23
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497 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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498
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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499 **Inputs**
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500
23
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501 **Count Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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502
27
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diff changeset
503 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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504
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
505 The following table gives some examples of factors and their levels:
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
506
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
507 ========= ============== ===============
15
d856341e03c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1
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diff changeset
508 Factor Factor level 1 Factor level 2
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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509 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
510 Treatment Treated Untreated
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
511 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
512 Condition Knockdown Wildtype
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
513 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
514 TimePoint Day4 Day1
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
515 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
516 SeqType SingleEnd PairedEnd
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
517 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
518 Gender Female Male
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
519 ========= ============== ===============
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
520
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
521 *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
iuc
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diff changeset
522
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
523 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
iuc
parents: 22
diff changeset
524
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
525 **Salmon or Sailfish Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
526
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
527 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
iuc
parents: 22
diff changeset
528
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
529 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
530
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
531 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
532 Name Length EffectiveLength TPM NumReads
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
533 ------------ ---------- --------------- ----------- -----------
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
534 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
535 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
536 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
parents: 22
diff changeset
537 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
iuc
parents: 22
diff changeset
538 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
parents: 22
diff changeset
539 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
diff changeset
540 NM_001198819 9527 7964.62 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
541 NM_001198820 9410 7855.78 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
542 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
iuc
parents: 22
diff changeset
543 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
544
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
545 **kallisto Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
546
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
547 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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parents: 22
diff changeset
548
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff changeset
549 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
550
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
551 ============ ========== =============== =========== ===========
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
552 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
iuc
parents: 22
diff changeset
553 ------------ ---------- --------------- ----------- -----------
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
554 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
parents: 26
diff changeset
555 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
parents: 26
diff changeset
556 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
parents: 26
diff changeset
557 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
parents: 26
diff changeset
558 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
iuc
parents: 22
diff changeset
559 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
iuc
parents: 26
diff changeset
560 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
561 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
parents: 26
diff changeset
562 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
iuc
parents: 22
diff changeset
563 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
564
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
565 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
566
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
567 **Output**
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
568
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
569 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
iuc
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diff changeset
570
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
571 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
572 Column Description
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
573 ------ ----------------------------------------------------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
574 1 Gene Identifiers
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
575 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
iuc
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diff changeset
576 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
iuc
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diff changeset
577 4 standard error estimate for the log2 fold change estimate
13
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents: 12
diff changeset
578 5 Wald statistic
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents: 12
diff changeset
579 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
iuc
parents: 12
diff changeset
580 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
iuc
parents:
diff changeset
581 which controls false discovery rate (FDR)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
582 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
583
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
584 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
585 .. _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
iuc
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diff changeset
586 ]]></help>
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
587 <citations>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
588 <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
iuc
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diff changeset
589 </citations>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
590 </tool>