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Add abspath value translation to data_manager_conf.xml.
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 04 Jun 2013 14:57:17 -0400
parents 11e84434ae70
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1 <?xml version="1.0"?>
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2 <data_managers>
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4 <data_manager tool_file="data_manager/bwa_index_builder.xml" id="bwa_index_builder" version="0.0.1">
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5 <data_table name="bwa_indexes">
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6 <output>
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7 <column name="value" />
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8 <column name="dbkey" />
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9 <column name="name" />
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10 <column name="path" output_ref="out_file" >
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11 <move type="directory" relativize_symlinks="True">
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12 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
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13 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bwa_index/${value}</target>
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14 </move>
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15 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwa_index/${value}/${path}</value_translation>
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16 <value_translation type="function">abspath</value_translation>
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17 </column>
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18 </output>
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19 </data_table>
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20 </data_manager>
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22 <data_manager tool_file="data_manager/bwa_color_space_index_builder.xml" id="bwa_color_space_index_builder" version="0.0.1">
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23 <data_table name="bwa_indexes_color">
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24 <output>
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25 <column name="value" />
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26 <column name="dbkey" />
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27 <column name="name" />
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28 <column name="path" output_ref="out_file" >
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29 <move type="directory" relativize_symlinks="True">
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30 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
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31 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bwa_index/${value}/color</target> <!-- confirm this as preferred location -->
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32 </move>
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33 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwa_index/${value}/color/${path}</value_translation>
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34 <value_translation type="function">abspath</value_translation>
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35 </column>
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36 </output>
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37 </data_table>
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38 </data_manager>
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40 </data_managers>