Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager_conf.xml @ 21:fd3fd1cae8dd draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
| author | dfornika |
|---|---|
| date | Mon, 04 Mar 2019 21:08:15 -0500 |
| parents | d04d198e185a |
| children | 7233538ef3cb |
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--- a/data_manager_conf.xml Fri Mar 01 17:38:11 2019 -0500 +++ b/data_manager_conf.xml Mon Mar 04 21:08:15 2019 -0500 @@ -1,44 +1,15 @@ <data_managers> - <data_manager tool_file="data_manager/kraken2_custom_database_builder.xml" id="kraken2_custom_database_builder" version="1.0"> - <data_table name="kraken2_databases"> - <output> - <column name="value"/> - <column name="name"/> - <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_database/${value}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_database/${value}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - </data_manager> - <data_manager tool_file="data_manager/kraken2_standard_database_builder.xml" id="kraken2_standard_database_builder" version="1.0"> - <data_table name="kraken2_databases"> - <output> - <column name="value"/> - <column name="name"/> - <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_database/${value}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_database/${value}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - </data_manager> <data_manager tool_file="data_manager/kraken2_build_standard.xml" id="kraken2_build_standard" version="1.0"> <data_table name="kraken2_databases"> <output> <column name="value"/> <column name="name"/> <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_database/${value}</target> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_database/${value}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> @@ -50,10 +21,27 @@ <column name="value"/> <column name="name"/> <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_database/${value}</target> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_database/${value}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + <data_manager tool_file="data_manager/kraken2_build_special.xml" id="kraken2_build_special" version="1.0"> + <data_table name="kraken2_databases"> + <output> + <column name="value"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>