Mercurial > repos > proteore > proteore_data_manager

annotate data_manager_conf.xml @ 60:da9e74d3c40d draft

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"planemo upload commit a69fdb4cdc110c75fea7439f0d97b67158c1bbbf"
author proteore
date Tue, 09 Jun 2020 13:19:26 +0000
parents 09d9fd9b2d8c
children
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1 <?xml version="1.0"?>
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2 <data_managers>
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3 <data_manager tool_file="data_manager/resource_building.xml" id="resource_building">
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4 <data_table name="proteore_peptide_atlas">
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5 <output>
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6 <column name="id"/>
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7 <column name="name" />
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8 <column name="tissue" />
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9 <column name="value" output_ref="output" >
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10 <move type="file">
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11 <!--source>${path}/${value}.tsv</source-->
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12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">peptide_atlas/</target>
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13 </move>
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14 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/peptide_atlas/${id}.tsv</value_translation>
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15 <value_translation type="function">abspath</value_translation>
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16 </column>
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17 </output>
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18 </data_table>
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19 <data_table name="proteore_protein_atlas_normal_tissue">
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20 <output>
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21 <column name="id"/>
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22 <column name="release"/>
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23 <column name="name" />
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24 <column name="tissue" />
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25 <column name="value" output_ref="output" >
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26 <move type="file">
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27 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
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28 </move>
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29 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
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30 <value_translation type="function">abspath</value_translation>
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31 </column>
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32 </output>
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33 </data_table>
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34 <data_table name="proteore_protein_atlas_rna_tissue">
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35 <output>
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36 <column name="id"/>
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37 <column name="release"/>
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38 <column name="name" />
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39 <column name="tissue" />
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40 <column name="value" output_ref="output" >
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41 <move type="file">
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42 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
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43 </move>
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44 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
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45 <value_translation type="function">abspath</value_translation>
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46 </column>
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47 </output>
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48 </data_table>
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49 <data_table name="proteore_protein_atlas_tumor_tissue">
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50 <output>
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51 <column name="id"/>
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52 <column name="release"/>
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53 <column name="name" />
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54 <column name="tissue" />
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55 <column name="value" output_ref="output" >
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56 <move type="file">
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57 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
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58 </move>
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59 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
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60 <value_translation type="function">abspath</value_translation>
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61 </column>
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62 </output>
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63 </data_table>
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64 <data_table name="proteore_protein_full_atlas">
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65 <output>
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66 <column name="id"/>
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67 <column name="release"/>
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68 <column name="name" />
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69 <column name="tissue" />
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70 <column name="value" output_ref="output" >
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71 <move type="file">
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72 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
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73 </move>
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74 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
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75 <value_translation type="function">abspath</value_translation>
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76 </column>
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77 </output>
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78 </data_table>
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79 <data_table name="proteore_id_mapping_Human">
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80 <output>
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81 <column name="id" />
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82 <column name="release"/>
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83 <column name="name" />
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84 <column name="species" />
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85 <column name="value" output_ref="output" >
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86 <move type="file">
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87 <!--source>${path}</source-->
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88 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
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89 </move>
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90 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
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91 <value_translation type="function">abspath</value_translation>
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92 </column>
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93 </output>
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94 </data_table>
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95 <data_table name="proteore_id_mapping_Mouse">
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96 <output>
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97 <column name="id" />
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98 <column name="release"/>
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99 <column name="name" />
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100 <column name="species" />
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101 <column name="value" output_ref="output" >
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102 <move type="file">
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103 <!--source>${path}</source-->
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104 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
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105 </move>
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106 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
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107 <value_translation type="function">abspath</value_translation>
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108 </column>
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109 </output>
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110 </data_table>
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111 <data_table name="proteore_id_mapping_Rat">
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112 <output>
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113 <column name="id" />
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114 <column name="release"/>
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115 <column name="name" />
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116 <column name="species" />
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117 <column name="value" output_ref="output" >
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118 <move type="file">
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119 <!--source>${path}</source-->
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120 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
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121 </move>
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122 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
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123 <value_translation type="function">abspath</value_translation>
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124 </column>
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125 </output>
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126 </data_table>
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127 <data_table name="proteore_biogrid_dictionaries">
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128 <output>
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129 <column name="id" />
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130 <column name="release"/>
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131 <column name="name" />
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132 <column name="species" />
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133 <column name="value" output_ref="output" >
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134 <move type="file">
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135 <!--source>${path}</source-->
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136 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
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137 </move>
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138 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
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139 <value_translation type="function">abspath</value_translation>
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140 </column>
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141 </output>
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142 </data_table>
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143 <data_table name="proteore_bioplex_dictionaries">
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144 <output>
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145 <column name="id" />
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146 <column name="release"/>
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147 <column name="name" />
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148 <column name="species" />
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149 <column name="value" output_ref="output" >
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150 <move type="file">
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151 <!--source>${path}</source-->
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152 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
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153 </move>
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154 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
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155 <value_translation type="function">abspath</value_translation>
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156 </column>
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157 </output>
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158 </data_table>
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159 <data_table name="proteore_humap_dictionaries">
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160 <output>
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161 <column name="id" />
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162 <column name="release"/>
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163 <column name="name" />
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164 <column name="species" />
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165 <column name="value" output_ref="output" >
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166 <move type="file">
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167 <!--source>${path}</source-->
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168 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
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169 </move>
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170 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
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171 <value_translation type="function">abspath</value_translation>
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172 </column>
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173 </output>
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174 </data_table>
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175 <data_table name="proteore_nextprot_ref">
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176 <output>
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177 <column name="id" />
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178 <column name="release"/>
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179 <column name="name" />
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180 <column name="value" output_ref="output" >
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181 <move type="file">
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182 <!--source>${path}</source-->
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183 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">proteore_nextprot_ref/</target>
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184 </move>
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185 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${release}.tsv</value_translation>
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186 <value_translation type="function">abspath</value_translation>
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187 </column>
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188 </output>
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189 </data_table>
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190 </data_manager>
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191 </data_managers>