Mercurial > repos > devteam > data_manager_bowtie2_index_builder
comparison data_manager_conf.xml @ 13:8bf75f813413 draft default tip
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 |
comparison
equal
deleted
inserted
replaced
| 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> |