Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 11:25204a860b79 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
author iuc
date Sun, 28 Jan 2018 04:04:12 -0500
parents 24a09ca67621
children bd06df00180a
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1 <tool id="deseq2" name="DESeq2" version="2.11.40">
0
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2 <description>Determines differentially expressed features from count tables</description>
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3 <requirements>
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4 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
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5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>
0
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6 </requirements>
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7 <stdio>
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8 <regex match="Execution halted"
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9 source="both"
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10 level="fatal"
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11 description="Execution halted." />
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12 <regex match="Error in"
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13 source="both"
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14 level="fatal"
7
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15 description="An undefined error occurred, please check your input carefully and contact your administrator." />
0
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16 <regex match="Fatal error"
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17 source="both"
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18 level="fatal"
7
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19 description="An undefined error occurred, please check your input carefully and contact your administrator." />
0
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20 </stdio>
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21 <version_command><![CDATA[
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22 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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23 ]]></version_command>
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24 <command><![CDATA[
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25 #if $tximport.tximport_selector == 'tximport':
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26 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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27 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
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28 #else:
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29 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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30 #end if
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31 #end if
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32
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33 #import json
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34 Rscript '${__tool_directory__}/deseq2.R'
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35 -o '$deseq_out'
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36 #if $pdf:
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37 -p '$plots'
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38 #end if
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39 #if $normCounts:
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40 -n '$counts_out'
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41 #end if
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42 #set $temp_factor_names = list()
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43 #for $factor in $rep_factorName:
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44 #set $temp_factor = list()
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45 #for $level in $factor.rep_factorLevel:
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46 #set $count_files = list()
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47 #for $file in $level.countsFile:
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48 $count_files.append(str($file))
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49 #end for
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50 $temp_factor.append( {str($level.factorLevel): $count_files} )
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51 #end for
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52 $temp_factor.reverse()
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53 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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54 #end for
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55 -f '#echo json.dumps(temp_factor_names)#'
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56 -t $fit_type
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57 #if $outlier_replace_off:
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58 -a
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59 #end if
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60 #if $outlier_filter_off:
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61 -b
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62 #end if
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63 #if $auto_mean_filter_off:
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64 -c
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65 #end if
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66 #if $many_contrasts:
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67 -m
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68 #end if
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69 #if $tximport.tximport_selector == 'tximport':
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70 -i
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71 -y $tximport.txtype
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72 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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73 -x mapping.gtf
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74 #else:
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75 -x mapping.txt
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76 #end if
5
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77
11
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78 #end if
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79 ]]></command>
0
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80 <inputs>
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81 <repeat name="rep_factorName" title="Factor" min="1">
6
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82 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
0
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83 help="Only letters, numbers and underscores will be retained in this field">
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84 <sanitizer>
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85 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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86 </sanitizer>
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87 </param>
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88 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
6
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89 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
0
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90 help="Only letters, numbers and underscores will be retained in this field">
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91 <sanitizer>
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92 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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93 </sanitizer>
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94 </param>
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95 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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96 </repeat>
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97 </repeat>
6
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98
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99 <conditional name="tximport">
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100 <param name="tximport_selector" type="select" label="Choice of Input data">
11
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101 <option value="count" selected="True">Count data (e.g. from HTSeq-count or featureCounts)</option>
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102 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
6
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103 </param>
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104 <when value="tximport">
11
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105 <param name="txtype" type="select" label="Program used to generate TPMs">
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106 <option value="kallisto">kallisto</option>
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107 <option value="sailfish">Sailfish</option>
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108 <option value="salmon">Salmon</option>
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109 </param>
6
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110 <conditional name="mapping_format">
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111 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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112 <option value="gtf" selected="True">GTF</option>
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113 <option value="tabular">Transcript-ID and Gene-ID mapping file</option>
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114 </param>
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115 <when value="gtf">
11
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116 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/>
6
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117 </when>
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118 <when value="tabular">
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119 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>
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120 </when>
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121 </conditional>
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122 </when>
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123 <when value="count" />
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124 </conditional>
0
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125 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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126 label="Visualising the analysis results"
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127 help="output an additional PDF files" />
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128 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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129 label="Output normalized counts table" />
0
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130 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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131 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
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132 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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133 <param name="fit_type" type="select" label="Fit type">
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134 <option value="1" selected="true">parametric</option>
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135 <option value="2">local</option>
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136 <option value="3">mean</option>
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137 </param>
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138 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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139 label="Turn off outliers replacement (only affects with >6 replicates)"
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140 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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141 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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142 or normalization factor for that sample" />
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143 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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144 label="Turn off outliers filtering (only affects with >2 replicates)"
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145 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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146 filter genes which contain a Cook’s distance above a cutoff" />
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147 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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148 label="Turn off independent filtering"
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149 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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150 </inputs>
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151 <outputs>
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152 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
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153 <filter>many_contrasts is False</filter>
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154 <actions>
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155 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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156 </actions>
0
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157 </data>
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158 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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159 <filter>many_contrasts is True</filter>
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160 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
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161 </collection>
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162 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
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163 <filter>pdf == True</filter>
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164 </data>
6
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165 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
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166 <filter>normCounts == True</filter>
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167 </data>
0
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168 </outputs>
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169 <tests>
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170 <!--Ensure tables output works-->
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171 <test expect_num_outputs="2">
0
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172 <repeat name="rep_factorName">
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173 <param name="factorName" value="Treatment"/>
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174 <repeat name="rep_factorLevel">
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175 <param name="factorLevel" value="Treated"/>
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176 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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177 </repeat>
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178 <repeat name="rep_factorLevel">
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179 <param name="factorLevel" value="Untreated"/>
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180 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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181 </repeat>
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182 </repeat>
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183 <param name="pdf" value="False"/>
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184 <param name="normCounts" value="True"/>
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185 <output name="counts_out" file="normalized_readcounts.tab"/>
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186 <output name="deseq_out" file="deseq2_out.tab"/>
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187 </test>
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188 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
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189 <test expect_num_outputs="1">
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190 <repeat name="rep_factorName">
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191 <param name="factorName" value="Treatment"/>
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192 <repeat name="rep_factorLevel">
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193 <param name="factorLevel" value="Treated"/>
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194 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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195 </repeat>
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196 <repeat name="rep_factorLevel">
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197 <param name="factorLevel" value="Untreated"/>
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198 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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199 </repeat>
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200 </repeat>
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201 <param name="pdf" value="False"/>
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202 <param name="tximport_selector" value="tximport"/>
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203 <param name="txtype" value="sailfish"/>
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204 <param name="mapping_format_selector" value="tabular"/>
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205 <param name="tabular_file" value="tx2gene.tab"/>
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206 <output name="deseq_out" file="sailfish/out_deseq2_sailfish.tab"/>
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207 </test>
0
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208 </tests>
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209 <help><![CDATA[
0
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210 .. class:: infomark
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211
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212 **What it does**
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213
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214 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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215
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216 -----
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217
0
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218 **Inputs**
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219
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220 **Count Files**
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221
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222 DESeq2_ takes count tables generated from **featureCounts** or **HTSeq-count** as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
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223
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224 The following table gives some examples of factors and their levels:
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225
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226 ========= ============== ===============
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227 Factor Factor level 1 Factor level 2
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228 --------- -------------- ---------------
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229 Treatment Treated Untreated
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230 --------- -------------- ---------------
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231 Condition Knockdown Wildtype
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232 --------- -------------- ---------------
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233 TimePoint Day4 Day1
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234 --------- -------------- ---------------
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235 SeqType SingleEnd PairedEnd
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236 --------- -------------- ---------------
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237 Gender Female Male
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238 ========= ============== ===============
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239
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240 *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.
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241
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242 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.
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243
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244 **Salmon or Sailfish Files**
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245
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246 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.
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247
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248 Example:
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249
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250 ============ ========== =============== =========== ===========
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251 Name Length EffectiveLength TPM NumReads
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252 ------------ ---------- --------------- ----------- -----------
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253 NR_001526 164 20.4518 0 0
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254 NR_001526_1 164 20.4518 0 0
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255 NR_001526_2 164 20.4518 0 0
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256 NM_130786 1764 1956.04 2.47415 109.165
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257 NR_015380 2129 2139.53 1.77331 85.5821
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258 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
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259 NM_001198819 9527 7964.62 0 0
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260 NM_001198820 9410 7855.78 0 0
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261 NM_014576 9267 7714.88 0.0481114 8.37255
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262 ============ ========== =============== =========== ===========
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263
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264 **kallisto Files**
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265
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266 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
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267
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268 Example:
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269
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270 ============ ========== =============== =========== ===========
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271 target_id length eff_length est_counts tpm
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272 ------------ ---------- --------------- ----------- -----------
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273 NR_001526 164 20.4518 0 0
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274 NR_001526_1 164 20.4518 0 0
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275 NR_001526_2 164 20.4518 0 0
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276 NM_130786 1764 1956.04 109.165 2.47415
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277 NR_015380 2129 2139.53 85.5821 1.77331
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278 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
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279 NM_001198819 9527 7964.62 0 0
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280 NM_001198820 9410 7855.78 0 0
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281 NM_014576 9267 7714.88 8.37255 0.0481114
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282 ============ ========== =============== =========== ===========
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283
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284 -----
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285
0
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286 **Output**
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287
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288 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
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289
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290 ====== ==========================================================
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291 Column Description
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292 ------ ----------------------------------------------------------
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293 1 Gene Identifiers
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294 2 mean normalised counts, averaged over all samples from both conditions
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295 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
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296 4 standard error estimate for the log2 fold change estimate
2
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297 5 Wald statistic
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298 6 p value for the statistical significance of this change
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299 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0
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300 which controls false discovery rate (FDR)
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301 ====== ==========================================================
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302
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303 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
11
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304 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
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305 ]]></help>
0
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306 <citations>
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307 <citation type="doi">10.1186/s13059-014-0550-8</citation>
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308 </citations>
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309 </tool>