Mercurial > repos > iuc > data_manager_build_bracken_database

annotate data_manager_conf.xml @ 6:a0f18c07696a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
author iuc
date Wed, 05 Nov 2025 13:31:43 +0000
parents 5bc823e95ed3
children
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
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1 <data_managers>
4
5bc823e95ed3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
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2 <data_manager tool_file="data_manager/bracken_build_database.xml" id="bracken_build_database">
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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3 <data_table name="bracken_databases">
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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4 <output>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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5 <column name="value"/>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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6 <column name="name"/>
6
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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7 <column name="path" output_ref="out_file">
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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8 <move type="directory" relativize_symlinks="True">
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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9 <!-- we move the top level folder, since the path points to the bracken DB file -->
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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10 <source>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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11 #import os
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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12 #set base_dir = os.path.dirname($path)
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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13 ${base_dir}
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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14 </source>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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15 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${value}</target>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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16 </move>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
diff changeset
17 <!-- we store the path to the bracken DB file, since this is what bracken uses -->
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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18 <value_translation>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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19 #import os
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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20 ${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${value}/${os.path.basename($path)}
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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21 </value_translation>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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22 <value_translation type="function">abspath</value_translation>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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23 </column>
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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24 </output>
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 4
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25
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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26 </data_table>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
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27 </data_manager>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
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28 </data_managers>