Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 25:a1aee7e3d092 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c2e762b248fa86bb844c8e2d136e127d701d7b5a
author iuc
date Wed, 21 Feb 2018 00:06:09 -0500
parents 1a34aec44d60
children 47267a044ef1
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1 <tool id="deseq2" name="DESeq2" version="2.11.40.1">
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>
25
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6 <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement>
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7 <requirement type="package" version="0.6.5">r-ggrepel</requirement>
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8 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
0
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9 </requirements>
6
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10 <stdio>
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11 <regex match="Execution halted"
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12 source="both"
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13 level="fatal"
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14 description="Execution halted." />
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15 <regex match="Error in"
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16 source="both"
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17 level="fatal"
19
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18 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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19 <regex match="Fatal error"
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20 source="both"
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21 level="fatal"
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22 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6
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23 </stdio>
23
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24 <version_command><![CDATA[
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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: ")
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26 ]]></version_command>
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27 <command><![CDATA[
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28 #if $tximport.tximport_selector == 'tximport':
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29 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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30 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
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31 #else:
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32 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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33 #end if
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34 #end if
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35
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36 #import json
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37 #import os
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38 Rscript '${__tool_directory__}/deseq2.R'
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39 -o '$deseq_out'
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40 #if $pdf:
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41 -p '$plots'
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42 #end if
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43 #if $normCounts:
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44 -n '$counts_out'
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45 #end if
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46 #set $filename_to_element_identifiers = {}
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47 #set $temp_factor_names = list()
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48 #for $factor in $rep_factorName:
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49 #set $temp_factor = list()
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50 #for $level in $factor.rep_factorLevel:
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51 #set $count_files = list()
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52 #for $file in $level.countsFile:
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53 $count_files.append(str($file))
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54 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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55 #end for
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56 $temp_factor.append( {str($level.factorLevel): $count_files} )
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57 #end for
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58 $temp_factor.reverse()
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59 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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60 #end for
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61 -f '#echo json.dumps(temp_factor_names)#'
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62 -l '#echo json.dumps(filename_to_element_identifiers)#'
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63 -t $fit_type
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64 #if $outlier_replace_off:
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65 -a
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66 #end if
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67 #if $outlier_filter_off:
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68 -b
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69 #end if
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70 #if $auto_mean_filter_off:
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71 -c
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72 #end if
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73 #if $many_contrasts:
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74 -m
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75 #end if
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76 #if $tximport.tximport_selector == 'tximport':
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77 -i
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78 -y $tximport.txtype
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79 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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80 -x mapping.gtf
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81 #else:
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82 -x mapping.txt
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83 #end if
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84
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85 #end if
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86 ]]></command>
0
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87 <inputs>
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88 <repeat name="rep_factorName" title="Factor" min="1">
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89 <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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90 help="Only letters, numbers and underscores will be retained in this field">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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91 <sanitizer>
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92 <valid initial="string.letters,string.digits"><add value="_" /></valid>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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93 </sanitizer>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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94 </param>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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95 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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96 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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97 help="Only letters, numbers and underscores will be retained in this field">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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98 <sanitizer>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
99 <valid initial="string.letters,string.digits"><add value="_" /></valid>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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100 </sanitizer>
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101 </param>
6
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102 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
0
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103 </repeat>
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104 </repeat>
17
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parents: 16
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105
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106 <conditional name="tximport">
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107 <param name="tximport_selector" type="select" label="Choice of Input data">
23
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108 <option value="count" selected="True">Count data (e.g. from HTSeq-count or featureCounts)</option>
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109 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
17
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110 </param>
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111 <when value="tximport">
23
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112 <param name="txtype" type="select" label="Program used to generate TPMs">
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113 <option value="kallisto">kallisto</option>
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114 <option value="sailfish">Sailfish</option>
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115 <option value="salmon">Salmon</option>
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116 </param>
17
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117 <conditional name="mapping_format">
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118 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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119 <option value="gtf" selected="True">GTF</option>
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120 <option value="tabular">Transcript-ID and Gene-ID mapping file</option>
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121 </param>
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122 <when value="gtf">
23
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123 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/>
17
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124 </when>
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125 <when value="tabular">
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126 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>
17
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127 </when>
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128 </conditional>
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129 </when>
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130 <when value="count" />
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131 </conditional>
0
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132 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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133 label="Visualising the analysis results"
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134 help="output an additional PDF files" />
17
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135 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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136 label="Output normalized counts table" />
0
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137 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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138 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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139 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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140 <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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141 <option value="1" selected="true">parametric</option>
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142 <option value="2">local</option>
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143 <option value="3">mean</option>
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144 </param>
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145 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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146 label="Turn off outliers replacement (only affects with >6 replicates)"
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147 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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148 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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149 or normalization factor for that sample" />
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150 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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151 label="Turn off outliers filtering (only affects with >2 replicates)"
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152 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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153 filter genes which contain a Cook’s distance above a cutoff" />
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154 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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155 label="Turn off independent filtering"
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156 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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157 </inputs>
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158 <outputs>
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159 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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160 <filter>many_contrasts is False</filter>
17
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161 <actions>
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162 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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163 </actions>
0
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164 </data>
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165 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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166 <filter>many_contrasts is True</filter>
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167 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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168 </collection>
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169 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
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170 <filter>pdf == True</filter>
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171 </data>
17
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172 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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173 <filter>normCounts == True</filter>
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174 </data>
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175 </outputs>
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176 <tests>
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177 <!--Ensure tables output works-->
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178 <test expect_num_outputs="2">
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179 <repeat name="rep_factorName">
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180 <param name="factorName" value="Treatment"/>
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181 <repeat name="rep_factorLevel">
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182 <param name="factorLevel" value="Treated"/>
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183 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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184 </repeat>
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185 <repeat name="rep_factorLevel">
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186 <param name="factorLevel" value="Untreated"/>
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187 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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188 </repeat>
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189 </repeat>
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190 <param name="pdf" value="False"/>
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191 <param name="normCounts" value="True"/>
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192 <output name="counts_out" file="normalized_readcounts.tab"/>
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193 <output name="deseq_out" file="deseq2_out.tab"/>
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194 </test>
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195 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
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196 <test expect_num_outputs="1">
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197 <repeat name="rep_factorName">
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198 <param name="factorName" value="Treatment"/>
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199 <repeat name="rep_factorLevel">
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200 <param name="factorLevel" value="Treated"/>
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201 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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202 </repeat>
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203 <repeat name="rep_factorLevel">
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204 <param name="factorLevel" value="Untreated"/>
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205 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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206 </repeat>
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207 </repeat>
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208 <param name="pdf" value="False"/>
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209 <param name="tximport_selector" value="tximport"/>
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210 <param name="txtype" value="sailfish"/>
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211 <param name="mapping_format_selector" value="tabular"/>
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212 <param name="tabular_file" value="tx2gene.tab"/>
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213 <output name="deseq_out" file="sailfish/out_deseq2_sailfish.tab"/>
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214 </test>
0
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215 </tests>
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216 <help><![CDATA[
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217 .. class:: infomark
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218
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219 **What it does**
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220
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221 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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222
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223 -----
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224
0
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225 **Inputs**
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226
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227 **Count Files**
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228
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229 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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230
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231 The following table gives some examples of factors and their levels:
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232
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233 ========= ============== ===============
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234 Factor Factor level 1 Factor level 2
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235 --------- -------------- ---------------
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236 Treatment Treated Untreated
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237 --------- -------------- ---------------
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238 Condition Knockdown Wildtype
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239 --------- -------------- ---------------
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240 TimePoint Day4 Day1
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241 --------- -------------- ---------------
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242 SeqType SingleEnd PairedEnd
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243 --------- -------------- ---------------
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244 Gender Female Male
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245 ========= ============== ===============
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246
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247 *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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248
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249 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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250
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251 **Salmon or Sailfish Files**
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252
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253 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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254
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255 Example:
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256
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257 ============ ========== =============== =========== ===========
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258 Name Length EffectiveLength TPM NumReads
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259 ------------ ---------- --------------- ----------- -----------
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260 NR_001526 164 20.4518 0 0
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261 NR_001526_1 164 20.4518 0 0
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262 NR_001526_2 164 20.4518 0 0
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263 NM_130786 1764 1956.04 2.47415 109.165
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264 NR_015380 2129 2139.53 1.77331 85.5821
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265 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
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266 NM_001198819 9527 7964.62 0 0
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267 NM_001198820 9410 7855.78 0 0
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268 NM_014576 9267 7714.88 0.0481114 8.37255
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269 ============ ========== =============== =========== ===========
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270
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271 **kallisto Files**
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272
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273 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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274
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275 Example:
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276
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277 ============ ========== =============== =========== ===========
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278 target_id length eff_length est_counts tpm
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279 ------------ ---------- --------------- ----------- -----------
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280 NR_001526 164 20.4518 0 0
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281 NR_001526_1 164 20.4518 0 0
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282 NR_001526_2 164 20.4518 0 0
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283 NM_130786 1764 1956.04 109.165 2.47415
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284 NR_015380 2129 2139.53 85.5821 1.77331
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285 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
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286 NM_001198819 9527 7964.62 0 0
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287 NM_001198820 9410 7855.78 0 0
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288 NM_014576 9267 7714.88 8.37255 0.0481114
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289 ============ ========== =============== =========== ===========
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290
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291 -----
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292
0
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293 **Output**
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294
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295 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
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296
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297 ====== ==========================================================
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298 Column Description
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299 ------ ----------------------------------------------------------
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300 1 Gene Identifiers
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301 2 mean normalised counts, averaged over all samples from both conditions
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302 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
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303 4 standard error estimate for the log2 fold change estimate
13
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304 5 Wald statistic
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305 6 p value for the statistical significance of this change
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306 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0
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307 which controls false discovery rate (FDR)
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308 ====== ==========================================================
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309
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310 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
23
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311 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
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312 ]]></help>
0
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313 <citations>
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314 <citation type="doi">10.1186/s13059-014-0550-8</citation>
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315 </citations>
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316 </tool>