Mercurial > repos > proteore > proteore_prot_features
annotate add_protein_features.xml @ 18:0a9ae3d7dbf2 draft default tip
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author | proteore |
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date | Thu, 20 Aug 2020 03:09:52 -0400 |
parents | 2952bae8a1ea |
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1 <tool id="prot_features" name="Add protein features" version="2020.08.17"> |
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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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24 |
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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="'"/> |
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44 </valid> |
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45 <mapping initial="none"> |
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46 <add source="'" target="__sq__"/> |
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47 <add source=" " target=""/> |
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48 <add source="
" target=""/> |
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49 <add source="
" target=""/> |
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50 <add source="	" 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="ProteinName" selected="false">Protein name</option> |
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70 <option value="SeqLength" selected="false">Sequence Length</option> |
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71 <option value="MW" selected="false">Molecular Weight</option> |
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72 <option value="IsoPoint" selected="false">Isoelectric point</option> |
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73 <option value="TMDomains" selected="false">Number of transmembrane domains</option> |
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74 <option value="SubcellLocations" selected="false">Subcellular Location</option> |
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75 <option value="Diseases" selected="false">Disease information</option> |
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76 <option value="Function" selected="false">Protein function</option> |
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77 <option value="PostTranslationalModifications" selected="false">Post translational modifications</option> |
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78 <option value="ProteinFamily" selected="false">Protein family</option> |
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79 <option value="Pathway" selected="false">Pathway(s)</option> |
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80 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> |
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81 <option value="Chr" selected="false">Chromosome</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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91 |
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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 and better inform 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. Only features/annotations assigned with a "GOLD" quality criterion are considered, otherwise a "NA" value is returned. |
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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 31-07-2020 (release Feb, 2020) |
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158 - nextProt release 07-05-2019 (release Feb, 2019) |
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159 - neXtProt release 08-10-2018 (release Feb, 2018) |
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160 |
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161 .. class:: warningmark |
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162 |
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163 For "Protein function", "Post translational modifications" and "Pathway(s)", only results with gold quality are returned. |
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164 |
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165 ----- |
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166 |
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167 .. class:: infomark |
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168 |
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169 **Authors** |
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170 |
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171 David Christiany, Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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172 |
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173 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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174 |
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175 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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176 |
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177 Help: contact@proteore.org for any questions or concerns about this tool. |
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178 |
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179 ]]></help> |
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180 <citations> |
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181 </citations> |
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182 |
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183 </tool> |