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annotate deseq2.xml @ 7:681fd2c5f47a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f-dirty
author iuc
date Sat, 05 Sep 2015 04:58:32 -0400
parents 982bd8bfa44c
children 6a8678140dd9
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5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1 <tool id="deseq2" name="DESeq2" version="2.1.8.0">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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2 <description>Determines differentially expressed features from count tables</description>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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3 <requirements>
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4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
3
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5 <requirement type="package" version="3.2.1">R</requirement>
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6 <requirement type="package" version="3.10.2">atlas</requirement>
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7 <requirement type="package" version="1.8.1">deseq2</requirement>
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8 </requirements>
6
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9 <stdio>
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10 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
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13 description="Execution halted." />
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
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14 <regex match="Error in"
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15 source="both"
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16 level="fatal"
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17 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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18 <regex match="Fatal error"
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19 source="both"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
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20 level="fatal"
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21 description="An undefined error occured, please check your intput carefully and contact your administrator." />
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
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22 </stdio>
2
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23 <version_command>
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24 <![CDATA[
6
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25 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
2
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26 ]]>
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27 </version_command>
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28 <command>
2
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29 <![CDATA[
0
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30 #import json
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31 Rscript \$DESEQ2_ROOT_PATH/script/deseq2.R
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32 -o "$deseq_out"
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33 #if $pdf:
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34 -p "$plots"
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35 #end if
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36 #set $temp_factor_names = list()
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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37 #for $factor in $rep_factorName:
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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38 #set $temp_factor = list()
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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39 #for $level in $factor.rep_factorLevel:
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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40 #set $count_files = list()
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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41 #for $file in $level.countsFile:
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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42 $count_files.append(str($file))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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43 #end for
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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44 $temp_factor.append( {str($level.factorLevel): $count_files} )
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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45 #end for
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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46 $temp_factor_names.append([str($factor.factorName), $temp_factor])
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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47 #end for
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48 -f '#echo json.dumps(temp_factor_names)#'
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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49 -t "$fit_type"
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50 #if $outlier_replace_off:
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51 -a
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52 #end if
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53 #if $outlier_filter_off:
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54 -b
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55 #end if
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56 #if $many_contrasts:
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57 -m
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58 #end if
2
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59 ]]>
0
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60 </command>
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61 <inputs>
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62 <repeat name="rep_factorName" title="Factor" min="1">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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63 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
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64 help="Only letters, numbers and underscores will be retained in this field">
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65 <sanitizer>
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66 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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67 </sanitizer>
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68 </param>
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69 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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70 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"
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71 help="Only letters, numbers and underscores will be retained in this field">
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72 <sanitizer>
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73 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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74 </sanitizer>
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75 </param>
6
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76 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
0
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77 </repeat>
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78 </repeat>
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79 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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80 label="Visualising the analysis results"
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81 help="output an additional PDF files" />
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82 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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83 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
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84 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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85 <param name="fit_type" type="select" label="Fit type">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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86 <option value="1" selected="true">parametric</option>
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87 <option value="2">local</option>
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88 <option value="3">mean</option>
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89 </param>
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90 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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91 label="Turn off outliers replacement (only affects with >6 replicates)"
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92 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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93 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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94 or normalization factor for that sample" />
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95 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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96 label="Turn off outliers filtering (only affects with >2 replicates)"
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97 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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98 filter genes which contain a Cook’s distance above a cutoff" />
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99 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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100 label="Turn off independent filtering"
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101 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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102 </inputs>
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103 <outputs>
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104 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
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105 <filter>many_contrasts is False</filter>
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106 </data>
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107 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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108 <filter>many_contrasts is True</filter>
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109 <discover_datasets pattern="vs" visible="true"/>
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110 </collection>
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111 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
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112 <filter>pdf == True</filter>
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113 </data>
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114 </outputs>
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115 <tests>
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116 <test>
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117 <repeat name="rep_factorName">
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118 <param name="factorName" value="Treatment"/>
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119 <repeat name="rep_factorLevel">
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120 <param name="factorLevel" value="Treated"/>
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121 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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122 </repeat>
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123 <repeat name="rep_factorLevel">
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124 <param name="factorLevel" value="Untreated"/>
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125 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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126 </repeat>
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127 </repeat>
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128 <param name="pdf" value="no"/>
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129 <output name="deseq_out" file="deseq2_out.tab"/>
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130 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/>
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131 </test>
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132 </tests>
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133 <help>
2
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134 <![CDATA[
0
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135 .. class:: infomark
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136
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137 **What it does**
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138
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139 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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140
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141
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142 **Inputs**
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143
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144 DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several 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.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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145
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146 The following table gives some examples of factors and their levels:
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147
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148 ========= ============== ===============
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149 Factor Factor level 1 Factor level 2
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150 --------- -------------- ---------------
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151 Treatment Treated Untreated
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152 --------- -------------- ---------------
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153 Condition Knockdown Wildtype
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154 --------- -------------- ---------------
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155 TimePoint Day4 Day1
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156 --------- -------------- ---------------
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157 SeqType SingleEnd PairedEnd
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158 --------- -------------- ---------------
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159 Gender Female Male
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160 ========= ============== ===============
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161
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162 *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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163
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164 **Output**
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165
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166 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
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167
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168 ====== ==========================================================
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169 Column Description
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170 ------ ----------------------------------------------------------
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171 1 Gene Identifiers
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172 2 mean normalised counts, averaged over all samples from both conditions
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173 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
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174 4 standard error estimate for the log2 fold change estimate
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175 5 p value for the statistical significance of this change
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176 6 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
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177 which controls false discovery rate (FDR)
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178 ====== ==========================================================
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181 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
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182 ]]>
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183 </help>
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184 <citations>
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185 <citation type="doi">10.1186/s13059-014-0550-8</citation>
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186 </citations>
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187 </tool>