Mercurial > repos > nate > data_manager_bowtie2_index_builder
diff data_manager_conf.xml @ 0:6220ea344019 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
| author | nate |
|---|---|
| date | Tue, 29 Jul 2025 17:13:06 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Jul 29 17:13:06 2025 +0000 @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/bowtie2_index_builder.xml" id="bowtie2_index_builder"> + <data_table name="bowtie2_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bowtie_index/v2/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + + <data_table name="tophat2_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <!-- no move, always happens as part of bowtie2 and uses that path --> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>