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1 <!--annotatePeaks - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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2 Copyright (C) 2015 Institut Curie
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3
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4 This program is free software: you can redistribute it and/or modify
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5 it under the terms of the GNU General Public License as published by
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6 the Free Software Foundation, either version 3 of the License, or
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7 (at your option) any later version.
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8
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9 This program is distributed in the hope that it will be useful,
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10 but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 GNU General Public License for more details.
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13
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14 You should have received a copy of the GNU General Public License
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15 along with this program. If not, see <http://www.gnu.org/licenses/>.-->
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16 <tool id="annotatePeaks" name="AnnotatePeaks" version="1.0">
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17 <description>Genomic annotation of Chip-Seq peaks</description>
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18 <requirements>
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19 <requirement type="package" version="2.11.1">fontconfig</requirement>
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20 <requirement type="package" version="3.1.2">R</requirement>
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21 </requirements>
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22 <command interpreter="bash">
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23 #if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotatePeaks_wrapper.sh -f $inputfile -y $log -m $minScore -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -y $log -c $controlfile -x $statsControl -o $outputPNG -m $minScore -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotatePeaks_wrapper.sh -y $log -f $inputfile -e $regfile -m $minScore -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -c $controlfile -x $statsControl -l $left -y $log -o $outputPNG -m $minScore -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotatePeaks_wrapper.sh -f $inputfile -y $log -m $minScore -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -y $log -c $controlfile -x $statsControl -o $outputPDF -m $minScore -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotatePeaks_wrapper.sh -y $log -f $inputfile -e $regfile -m $minScore -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -c $controlfile -x $statsControl -l $left -y $log -o $outputPDF -m $minScore -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 1#end if
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24 </command>
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25 <inputs>
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26
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27 <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/>
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28 <param name="minScore" type="float" label="MinimalScore" value="0" help="Set to 0 if you don't want to filter your .BED file with peaks"/>
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29
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30 <conditional name="use_control">
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31 <param name="use_control_selector" type="select" label="Use control data">
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32 <option value="no" selected="true">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <when value="yes">
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36 <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/>
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37 </when>
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38 </conditional>
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39
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40 <param name="left" type="integer" label="Define Promoter is a region up to X bp upstream gene TSS" value="-2000"/>
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41 <param name="right" type="integer" label="Define Immediate Downstream is a region up to X bp downstream gene TSS" value="2000"/>
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42 <param name="EnhLeft" type="integer" label="Define Enhancer is a region up to X bp upstream gene TSS" value="-30000"/>
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43 <param name="DownGene" type="integer" label="Define Gene Downstream is a region up to X bp downstream transcription end" value="5000"/>
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44
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45
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46 <conditional name="input_organism">
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47 <param name="input_organism_selector" type="select" label="Select organism">
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48 <option value="Human" selected="true">Homo sapiens</option>
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49 <option value="Mouse">Mus musculus</option>
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50 <option value="Zebrafish">Zebrafish (Danio rerio)</option>
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51 <option value="XTropicalis">X.Tropicalis</option>
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52 <option value="Bacteria/MycoTube">M. tuberculosis</option>
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53 </param>
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54 <when value="Human">
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55 <param name="version" type="select" label="Select genome vesion">
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56 <option value="hg19" selected="true">hg19</option>
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57 <option value="hg18">hg18</option>
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58 </param>
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59 </when>
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60 <when value="Mouse">
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61 <param name="version" type="select" label="Select genome vesion">
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62 <option value="mm8" >mm8</option>
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63 <option value="mm9" selected="true">mm9</option>
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64 <option value="mm10" >mm10</option>
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65 </param>
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66 </when>
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67 <when value="Zebrafish">
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68 <param name="version" type="select" label="Select genome vesion">
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69 <option value="zv9" selected="true">zv9</option>
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70 </param>
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71 </when>
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72 <when value="XTropicalis">
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73 <param name="version" type="select" label="Select genome vesion">
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74 <option value="xenTro2" >xenTro2</option>
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75 <option value="xenTro3" selected="true">xenTro3</option>
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76 </param>
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77 </when>
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78 <when value="Bacteria/MycoTube">
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79 <param name="version" type="select" label="Select genome vesion">
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80 <option value="H37Rv" selected="true">H37Rv</option>
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81 </param>
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82 </when>
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83 </conditional>
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84
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85 <conditional name="use_reg">
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86 <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)">
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87 <option value="no" selected="true">No</option>
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88 <option value="yes">Yes</option>
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89 </param>
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90 <when value="yes">
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91 <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/>
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92 </when>
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93 </conditional>
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94
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95 <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/>
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96 </inputs>
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97 <outputs>
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98 <data name="outputPNG" format="png" label="Peaks Stats (png)">
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99 <filter>(if_PDF == 0)</filter>
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100 </data>
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101 <data name="outputPDF" format="pdf" label="Peaks Stats (pdf)">
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102 <filter>(if_PDF == True)</filter>
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103 </data>
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104
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105 <data name="stats" format="tabular" label="Annotated Peaks (ChIP)"/>
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106 <data name="log" format="log" label=".LOG for Annotated Peaks"/>
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107 <data name="statsControl" format="tabular" label="Annotated Peaks (Control)">
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108 <filter>(use_control['use_control_selector'] == 'yes')</filter>
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109 </data>
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110 </outputs>
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111 <tests>
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112 <test>
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113 <param name="inputfile" value="peaks_test.bed"/>
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114 <param name="minScore" value="0.0"/>
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115 <param name="use_control_selector" value="yes"/>
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116 <param name="controlfile" value="peaks_control.bed"/>
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117 <param name="left" value="-2000"/>
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118 <param name="right" value="2000"/>
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119 <param name="EnhLeft" value="-30000"/>
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120 <param name="DownGene" value="5000"/>
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121 <param name="input_organism_selector" value="Mouse"/>
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122 <param name="version" value="mm9"/>
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123 <param name="use_reg_selector" value="yes"/>
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124 <param name="regfile" value="Probesets_FC1.5_10022011.txt"/>
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125 <param name="if_PDF" value="1"/>
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126 <output name="outputPDF" file="test_annotatePeaks_1.dat" ftype="pdf"/>
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127 <output name="stats" file="test_annotatePeaks_2.dat" ftype="tabular"/>
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128 <output name="log" file="test_annotatePeaks_3.dat" ftype="log"/>
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129 <output name="statsControl" file="test_annotatePeaks_4.dat" ftype="tabular"/>
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130 </test>
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131 </tests>
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132 <help>
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133 **What it does**
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134
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135 This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution
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136
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137 </help>
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138 <citations>
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139 <citation type="bibtex">@article{Boeva01102012,
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140 author = {Boeva, Valentina and Lermine, Alban and Barette, Camille and Guillouf, Christel and Barillot, Emmanuel},
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141 title = {Nebula—a web-server for advanced ChIP-seq data analysis},
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142 volume = {28},
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143 number = {19},
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144 pages = {2517-2519},
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145 year = {2012},
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146 doi = {10.1093/bioinformatics/bts463},
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147 URL = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.abstract},
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148 eprint = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.full.pdf+html},
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149 journal = {Bioinformatics}
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150 }</citation>
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151 </citations>
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152 </tool>
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