Mercurial > repos > devteam > data_manager_bowtie2_index_builder

annotate data_manager_conf.xml @ 1:9bf4eb559ed5 draft

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planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
author devteam
date Mon, 10 Aug 2015 16:44:10 -0400
parents 9458af1ab90b
children e87aeff2cf88
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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/bowtie2_index_builder.xml" id="bowtie2_index_builder" version="0.0.2">
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5 <data_table name="bowtie2_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}">${dbkey}/bowtie2_index/${value}</target>
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14 </move>
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15 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_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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21 <data_table name="tophat2_indexes">
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22 <output>
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23 <column name="value" />
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24 <column name="dbkey" />
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25 <column name="name" />
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26 <column name="path" output_ref="out_file" >
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27 <!-- no move, always happens as part of bowtie2 and uses that path -->
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28 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation>
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29 <value_translation type="function">abspath</value_translation>
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30 </column>
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31 </output>
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32 </data_table>
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33 </data_manager>
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35 </data_managers>