Mercurial > repos > devteam > data_manager_bowtie2_index_builder

comparison data_manager_conf.xml @ 13:8bf75f813413 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author iuc
date Thu, 05 Dec 2024 06:46:58 +0000
parents 16230154ee87
children
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12:16230154ee87 13:8bf75f813413
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <data_managers> 2 <data_managers>
3
4 <data_manager tool_file="data_manager/bowtie2_index_builder.xml" id="bowtie2_index_builder"> 3 <data_manager tool_file="data_manager/bowtie2_index_builder.xml" id="bowtie2_index_builder">
5 <data_table name="bowtie2_indexes"> 4 <data_table name="bowtie2_indexes">
6 <output> 5 <output>
7 <column name="value" /> 6 <column name="value" />
8 <column name="dbkey" /> 7 <column name="dbkey" />
9 <column name="name" /> 8 <column name="name" />
10 <column name="path" output_ref="out_file" > 9 <column name="path" output_ref="out_file" >
11 <move type="directory" relativize_symlinks="True"> 10 <move type="directory" relativize_symlinks="True">
12 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> 11 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
13 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bowtie2_index/${value}</target> 12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bowtie_index/v2/${value}</target>
14 </move> 13 </move>
15 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation> 14 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${path}</value_translation>
16 <value_translation type="function">abspath</value_translation> 15 <value_translation type="function">abspath</value_translation>
17 </column> 16 </column>
18 </output> 17 </output>
19 </data_table> 18 </data_table>
20 19
23 <column name="value" /> 22 <column name="value" />
24 <column name="dbkey" /> 23 <column name="dbkey" />
25 <column name="name" /> 24 <column name="name" />
26 <column name="path" output_ref="out_file" > 25 <column name="path" output_ref="out_file" >
27 <!-- no move, always happens as part of bowtie2 and uses that path --> 26 <!-- no move, always happens as part of bowtie2 and uses that path -->
28 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation> 27 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${path}</value_translation>
29 <value_translation type="function">abspath</value_translation> 28 <value_translation type="function">abspath</value_translation>
30 </column> 29 </column>
31 </output> 30 </output>
32 </data_table> 31 </data_table>
33 </data_manager> 32 </data_manager>
34
35 </data_managers> 33 </data_managers>