Mercurial > repos > matthias > data_manager_dada2

annotate data_manager/dada2_fetcher.xml @ 4:51b90d282704 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 2f47c03d1b775ab796c75c806c1ab247bb51359d
author matthias
date Fri, 10 May 2019 11:52:03 -0400
parents 3a4ee8bf012a
children b899349a9c2b
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1 <?xml version="1.0"?>
4
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2 <tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.5">
3
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3 <description>Download reference databases</description>
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4 <command detect_errors="exit_code"><![CDATA[
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5 python '$__tool_directory__/data_manager.py'
4
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6 --out '$out_file'
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matthias
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7 #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select)
51b90d282704 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 2f47c03d1b775ab796c75c806c1ab247bb51359d
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8 --dataset '$dataset'
1
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9 ]]>
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10 </command>
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11 <inputs>
3
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12 <conditional name="db_cond">
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13 <param name="db_select" type="select" label="Taxonomic database">
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14 <option value="silva">Silva</option>
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15 <option value="rdp">RDP</option>
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16 <option value="greengenes">GreenGenes</option>
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17 <option value="unite">UNITE: General Fasta</option>
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18 <option value="RefSeq_RDP">NCBI RefSeq 16S rRNA database supplemented by RDP</option>
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19 <option value="gtdb">GTDB: Genome Taxonomy Database (Bacteria &amp; Archaea)</option>
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20 <option value="hitdb">HitDB (Human InTestinal 16S)</option>
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21 <option value="silva_euk_18S">Silva Eukaryotic 18S</option>
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22 <option value="PR2">Protist Ribosomal Reference database (PR2)</option>
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23 </param>
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24 <when value="silva">
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25 <param name="version_select" type="select" label="Database version">
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26 <option value="132">132</option>
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27 <option value="128">128</option>
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28 </param>
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29 </when>
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30 <when value="rdp">
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31 <param name="version_select" type="select" label="Database version">
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32 <option value="16">16</option>
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33 <option value="14">14</option>
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34 </param>
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35 </when>
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36 <when value="greengenes">
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37 <param name="version_select" type="select" label="Database version">
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38 <option value="13.84">13.84</option>
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39 </param>
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40 </when>
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41 <when value="unite">
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42 <param name="version_select" type="select" label="Database version">
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43 <option value="8.0_fungi">release 8.0 for Fungi</option>
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44 <option value="8.0_fungi_singleton">release 8.0 for Fungi including global and 97% singletons</option>
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45 </param>
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46 </when>
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47 <when value="RefSeq_RDP">
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48 <param name="version_select" type="select" label="Database version">
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49 <option value="2018_05">05/2018</option>
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50 </param>
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51 </when>
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52 <when value="gtdb">
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53 <param name="version_select" type="select" label="Database version">
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54 <option value="2018_11">11/2018</option>
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55 </param>
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56 </when>
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57 <when value="hitdb">
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58 <param name="version_select" type="select" label="Database version">
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59 <option value="1">1</option>
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60 </param>
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61 </when>
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62 <when value="silva_euk_18S">
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63 <param name="version_select" type="select" label="Database version">
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64 <option value="132">132</option>
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65 </param>
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66 </when>
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67 <when value="PR2">
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68 <param name="version_select" type="select" label="Database version">
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69 <option value="4.11.1">4.11.1</option>
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70 </param>
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71 </when>
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72 </conditional>
1
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73 </inputs>
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74 <outputs>
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75 <data name="out_file" format="data_manager_json" />
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76 </outputs>
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77 <tests>
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78 <test>
3
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79 <param name="db_cond|db_select" value="silva"/>
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80 <param name="db_cond|version_select" value="132"/>
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81 <output name="out_file" file="silva132_json"/>
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82 </test>
3
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83 <test>
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84 <param name="db_cond|db_select" value="rdp"/>
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85 <param name="db_cond|version_select" value="16"/>
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86 <output name="out_file" file="rdp16_json"/>
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87 </test>
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88 <test>
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89 <param name="db_cond|db_select" value="greengenes"/>
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90 <param name="db_cond|version_select" value="13.84"/>
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91 <output name="out_file" file="greengenes13.84_json"/>
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92 </test>
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93 <test>
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94 <param name="db_cond|db_select" value="unite"/>
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95 <param name="db_cond|version_select" value="8.0_fungi"/>
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96 <output name="out_file" file="unite8fungi_json"/>
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97 </test>
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98 <test>
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99 <param name="db_cond|db_select" value="RefSeq_RDP"/>
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100 <param name="db_cond|version_select" value="2018_05"/>
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101 <output name="out_file" file="RefSeq_RDP2018_json"/>
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102 </test>
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103 <test>
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104 <param name="db_cond|db_select" value="gtdb"/>
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105 <param name="db_cond|version_select" value="2018_11"/>
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106 <output name="out_file" file="gtdb2018_json"/>
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107 </test>
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108 <test>
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109 <param name="db_cond|db_select" value="hitdb"/>
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110 <param name="db_cond|version_select" value="1"/>
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111 <output name="out_file" file="hitdb1_json"/>
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112 </test>
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113 <test>
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114 <param name="db_cond|db_select" value="silva_euk_18S"/>
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115 <param name="db_cond|version_select" value="132"/>
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116 <output name="out_file" file="silvaeuk132_json"/>
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117 </test>
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118 <test>
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119 <param name="db_cond|db_select" value="PR2"/>
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120 <param name="db_cond|version_select" value="4.11.1"/>
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121 <output name="out_file" file="PR24.11.1_json"/>
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122 </test>
1
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123 </tests>
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124 <help><![CDATA[
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125 Public Reference databases maintained by the DADA2 project
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126 ..........................................................
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127
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128 The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available
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129
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130 - Silva (https://www.arb-silva.de/)
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131 - RDP (http://rdp.cme.msu.edu/)
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132 - GreenGenes (http://greengenes.secondgenome.com/)
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133 - UNITE general FASTA (https://unite.ut.ee/repository.php)
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134
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135 While Silva and RDP contain reference databases for taxonomy and species assignment, the greengenes and UNITE databases only contains a reference database for taxonomy assignment.
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136
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137 For the Silva databases check the license information: http://www.arb-silva.de/silva-license-information.
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138
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139 Except for UNITE all reference databases are downloaded from the corresponding zenodo links that are listed on the DADA2 website. The UNITE databases are taken from the links provided on the UNITE website
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140
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141 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
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142
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143 Further public Reference databases listed by the DADA2 project
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144 ..............................................................
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145
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146 Several contributed reference databases are listed of the DADA2 project website (https://benjjneb.github.io/dada2/training.html):
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147
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148 - RefSeq + RDP (NCBI RefSeq 16S rRNA database supplemented by RDP)
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149 - GTDB: Genome Taxonomy Database (More info: http://gtdb.ecogenomic.org/)
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150 - HitDB version 1 (Human InTestinal 16S rRNA) (https://github.com/microbiome/HITdb)
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151 - RDP fungi LSU
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152 - Silva Eukaryotic 18S
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153 - PR2 (https://github.com/pr2database/pr2database)
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154
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155 Except for PR2, all reference databases are downloaded from the corresponding zenodo links that are listed on the DADA2 website. The PR2 database is taken from their github page.
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156
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157 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
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158 ]]></help>
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159 <citations>
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160 <!-- silva -->
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161 <citation type="doi">10.1093/nar/gks1219</citation>
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162 <!-- rdp -->>
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163 <citation type="doi">10.1093/nar/gkt1244</citation>
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164 <!-- greengenes -->
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165 <citation type="doi">10.1128/AEM.03006-05</citation>
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166 <!-- unite -->
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167 <citation type="doi">10.15156/BIO/786343</citation>
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168 <!-- TODO gtdb ??? -->
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169 <!-- hitdb -->
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170 <citation type="doi">10.1186/s12864-015-2265-y</citation>
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171 <!-- PR2 -->
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172 <citation type="doi">10.1093/nar/gks1160</citation>
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173 </citations>
1
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174 </tool>
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175