Mercurial > repos > proteore > proteore_expression_rnaseq_abbased
annotate add_expression_data.xml @ 15:208b87582b4c draft default tip
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author | proteore |
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date | Wed, 29 Apr 2020 08:51:13 -0400 |
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1 <tool id="rna_abbased_data" name="Add expression data" version="2020.04.06"> |
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2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas] |
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3 </description> |
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4 <requirements> |
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5 <requirement type="package" version="3.6.1">r-base</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 $__tool_directory__/add_expression_HPA.R |
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13 --input='$inputtype.genelist' |
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14 --select='$options.hpaparams' |
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15 --output='$output' |
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16 |
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17 #if $inputtype.filetype == "copy_paste": |
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18 --inputtype="copypaste" |
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19 #else |
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20 --inputtype="tabfile" |
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21 --header='$inputtype.header' |
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22 --column='$inputtype.column' |
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23 #end if |
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24 |
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25 #if "protein_atlas" in str($ref_file).split("/") |
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26 --atlas="$ref_file" |
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27 #else |
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28 --atlasf="$__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 <param name="ref_file" type="select" label="HPA source file version" > |
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35 <options from_data_table="proteore_protein_full_atlas"> |
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36 <filter type="sort_by" column="0"/> |
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37 </options> |
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38 </param> |
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39 <conditional name="inputtype"> |
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40 <param name="filetype" type="select" label="Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787)" help="Copy/paste or from a file (e.g. table)"> |
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41 <option value="file_all" selected="true">Input file containing your IDs</option> |
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42 <option value="copy_paste">Copy/paste your list of IDs</option> |
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43 </param> |
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44 <when value="copy_paste"> |
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45 <param name="genelist" type="text" label="Enter a list of IDs"> |
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46 <sanitizer> |
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47 <valid initial="string.printable"> |
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48 <remove value="'"/> |
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49 </valid> |
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50 <mapping initial="none"> |
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51 <add source="'" target="__sq__"/> |
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52 </mapping> |
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53 </sanitizer> |
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54 </param> |
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55 </when> |
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56 <when value="file_all"> |
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57 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> |
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58 <param name="column" type="text" label="Column IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"> |
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59 <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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60 </param> |
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61 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?"/> |
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62 </when> |
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63 </conditional> |
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64 <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> |
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65 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" > |
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66 <option value="Gene" selected="true">Gene name</option> |
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67 <option value="Gene description" selected="false">Gene description</option> |
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68 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> |
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69 <option value="Antibody">Antibody reference</option> |
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70 <option value="RNA tissue specificity">RNA tissue category</option> |
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71 <option value="Reliability (IH)">IH detection level</option> |
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72 <option value="Reliability (IF)">IF detection level</option> |
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73 <option value="Subcellular location">Subcellular location</option> |
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74 <option value="RNA tissue specific NX">RNA tissue specificity abundance in 'Transcript Per Million'</option> |
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75 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million' (only for 23/10/2018 release)</option> |
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76 </param> |
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77 </section> |
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78 |
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79 </inputs> |
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80 |
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81 |
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82 <outputs> |
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83 <data name="output" format="tsv" label=""/> |
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84 </outputs> |
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85 |
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86 <tests> |
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87 <test> |
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88 <conditional name="inputtype"> |
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89 <param name="filetype " value="file_all"/> |
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90 <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/> |
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91 <param name="column" value="c8"/> |
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92 <param name="header" value="true"/> |
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93 </conditional> |
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94 <section name="options"> |
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95 <param name="hpaparams" value="Gene,Gene description,Evidence,Antibody,RNA tissue category,Reliability (IH),Reliability (IF),Subcellular location,RNA TS TPM,TPM max in non-specific"/> |
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96 </section> |
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97 <output name="output" file="Get_annotation_RNAseq.txt"/> |
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98 </test> |
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99 </tests> |
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100 |
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101 <help><![CDATA[ |
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102 **Description** |
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103 |
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104 This tool adds expression annotation (RNAseq- or antibody-based experimental data - see "Parameters" below) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your gene/protein list. |
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105 |
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106 ----- |
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107 |
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108 **Input** |
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109 |
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110 Input can be either a list of Ensembl gene (ENSG) IDs (copy/paste mode) or a file containing multiple fields with at least one column of Ensembl gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs. |
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111 |
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112 .. class:: warningmark |
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113 |
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114 In copy/paste mode, the number of IDs considered in input is limited to 5000. |
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115 |
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116 ----- |
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117 |
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118 **Parameters** |
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119 |
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120 "Select information to add to your list": choose by clicking the following information: |
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121 |
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122 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) |
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123 |
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124 - Gene description: entry description (full text) |
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125 |
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126 - Evidence: at protein level, at transcript level or no evidence |
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127 |
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128 - Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF |
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129 |
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130 - RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna . |
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131 |
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132 - IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if . |
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133 |
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134 - IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih . |
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135 |
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136 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa |
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137 |
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138 - RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. |
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139 |
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140 - RNA non-specific tissue abundance in 'Transcript Per Million' (only available from 23/10/2018 release): please refer to http://www.proteinatlas.org/about/assays+annotation#rna. |
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141 |
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142 ----- |
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143 |
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144 **Output** |
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145 |
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146 The output is a tabular file containing initial columns and new columns with annotation from HPA. |
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147 |
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148 ----- |
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149 |
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150 **HPA source file version (release date)** |
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151 |
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152 Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38 |
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153 |
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154 Release date 21/01/2020: a subset of the data in the Human Protein Atlas version 19.1 |
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155 |
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156 downloaded from: http://www.proteinatlas.org/download/proteinatlas.tab.gz |
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157 |
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158 ----- |
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159 |
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160 .. class:: infomark |
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161 |
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162 **Authors** |
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163 |
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164 Lisa Perus, David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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165 |
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166 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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167 |
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168 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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169 |
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170 Help: contact@proteore.org for any questions or concerns about this tool. |
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171 |
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172 ]]></help> |
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173 |
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174 <citations> |
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175 </citations> |
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176 |
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177 </tool> |