Mercurial > repos > proteore > proteore_prot_features

annotate add_protein_features.xml @ 19:381e18f13ed2 draft

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"planemo upload commit 6a3a63d9870148e6fee84e771db614f9da9a8245-dirty"
author proteore
date Thu, 30 Jul 2020 09:45:47 +0000
parents bdbc7620e804
children 3c5813b29486
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1 <tool id="prot_features" name="Add protein features" version="2020.07.30.1">
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2 <description>[neXtProt, Human]
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="3.4.1">R</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11
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12 Rscript $__tool_directory__/add_protein_features.R
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13 --inputtype="$inputtype.filetype"
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14 --input='$inputtype.genelist'
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15
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16 #if $inputtype.filetype == "file"
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17 --column='$inputtype.column'
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18 --header=$inputtype.header
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19 #end if
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20
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21 --type='$idtype'
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22 --pc_features='$pc_features'
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23 --output='$output'
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25 #if 'proteore_nextprot_ref' in str($ref_file).split("/")
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26 --nextprot="$ref_file"
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27 #else
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28 --nextprot="$__tool_directory__/$ref_file"
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29 #end if
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30
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31 ]]></command>
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32
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33 <inputs>
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34 <conditional name="inputtype">
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35 <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt; e.g. NX_P05090 or P05090)" help="Copy/paste or from a file" >
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36 <option value="file" selected="true">Input file containing your IDs </option>
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37 <option value="copy_paste">Copy/paste your list of IDs</option>
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38 </param>
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39 <when value="copy_paste">
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40 <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0">
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41 <sanitizer invalid_char="">
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42 <valid initial="string.printable">
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43 <remove value="&apos;"/>
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44 </valid>
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45 <mapping initial="none">
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46 <add source="&apos;" target="__sq__"/>
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47 <add source="&#x20;" target=""/>
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48 <add source="&#xA;" target=""/>
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49 <add source="&#xD;" target=""/>
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50 <add source="&#x9;" target=""/>
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51 </mapping>
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52 </sanitizer>
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53 </param>
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54 </when>
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55 <when value="file">
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56 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
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57 <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1">
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58 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
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59 </param>
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60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
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61 </when>
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62 </conditional>
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63
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64 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false">
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65 <option value="NextprotID" selected="true">neXtProt IDs</option>
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66 <option value="Uniprot_AC" selected="false">UniProt accession number</option>
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67 </param>
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68 <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
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69 <option value="SeqLength" selected="false">Sequence Length</option>
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70 <option value="MW" selected="false">Molecular Weight</option>
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71 <option value="IsoPoint" selected="false">Isoelectric point</option>
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72 <option value="TMDomains" selected="false">Number of transmembrane domains</option>
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73 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
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74 <option value="Chr" selected="false">Chromosome</option>
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75 <option value="SubcellLocations" selected="false">Subcellular Location</option>
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76 <option value="Diseases" selected="false">Disease information</option>
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77 <option value="ProteinName" selected="false">Protein name</option>
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78 <option value="Function" selected="false">Protein function</option>
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79 <option value="PostTranslationalModifications" selected="false">Post translational modifications</option>
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80 <option value="ProteinFamily" selected="false">Protein family</option>
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81 <option value="Pathway" selected="false">Pathway(s)</option>
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82 </param>
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83
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84 <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
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85 <options from_data_table="proteore_nextprot_ref">
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86 <filter type="sort_by" column="0"/>
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87 </options>
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88 </param>
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89
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90 </inputs>
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92
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93 <outputs>
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94 <data name="output" format="tsv" label="Add_information_from_neXtProt on ${inputtype.genelist.name}">
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95 <filter>inputtype=="file"</filter>
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96 </data>
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97 <data name="output" format="tsv" label="Add_information_from_neXtProt"/>
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98 </outputs>
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99
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100 <tests>
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101 <test>
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102 <conditional name="inputtype">
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103 <param name="filetype" value="file"/>
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104 <param name="genelist" value="Lacombe_et_al_2017.tsv"/>
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105 <param name="column" value="c1"/>
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106 <param name="header" value="true"/>
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107 </conditional>
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108
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109 <param name="idtype" value="Uniprot_AC"/>
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110 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/>
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111
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112 <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/>
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113 <output name="output" file="Add_information_from_neXtProt.tsv"/>
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114 </test>
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115 </tests>
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116
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117 <help><![CDATA[
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118
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119 **Description**
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120
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121 This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list.
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122
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123 -----
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124
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125 **Input**
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126
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127 A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool.
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128
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129 .. class:: warningmark
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130
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131 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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132
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133 -----
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134
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135 **Parameters**
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136
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137 "Select features": select each feature of your interest by clicking the corresponding checkbox. Disease information is set to "Yes" by default.
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138
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139 -----
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140
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141 **Output**
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142
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143 Output is a tabular file containing both original columns and new columns including the annotation requested.
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144
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145 .. class:: warningmark
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146
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147 "Protein name","Protein function","Post translational modifications","Protein family","Pathway(s)" options will not work will releases older than 08/2020.
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148
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149 -----
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150
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151 **Data source (release date)**
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152
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153 Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017)
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154
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155 neXtProt releases :
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156
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157 - nextProt release 07-05-2019 (release Feb 13, 2019)
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158 - neXtProt release 08-10-2018 (release Feb 21, 2018)
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159
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160 .. class:: warningmark
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161
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162 For "Protein function", "Post translational modifications" and "Pathway(s)", only results with gold quality are returned.
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163
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164 -----
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165
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166 .. class:: infomark
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167
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168 **Authors**
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169
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170 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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171
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172 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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173
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174 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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175
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176 Help: contact@proteore.org for any questions or concerns about this tool.
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177
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178 ]]></help>
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179 <citations>
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180 </citations>
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181
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182 </tool>