Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 9:1601703ae511 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 20:09:07 -0500 |
| parents | f53064ca5398 |
| children | d0b9df6c21dd |
| files | data_manager/kraken2_build_special.py data_manager/kraken2_build_standard.py data_manager_conf.xml |
| diffstat | 3 files changed, 20 insertions(+), 16 deletions(-) [+] |
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--- a/data_manager/kraken2_build_special.py Mon Mar 04 19:24:23 2019 -0500 +++ b/data_manager/kraken2_build_special.py Mon Mar 04 20:09:07 2019 -0500 @@ -96,13 +96,15 @@ else: raise + data_manager_output = {} + kraken2_build_standard( - data_manager_input, + data_manager_output, kraken2_args, target_directory, ) - open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input)) + open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) if __name__ == "__main__":
--- a/data_manager/kraken2_build_standard.py Mon Mar 04 19:24:23 2019 -0500 +++ b/data_manager/kraken2_build_standard.py Mon Mar 04 20:09:07 2019 -0500 @@ -93,13 +93,15 @@ else: raise + data_manager_output = {} + kraken2_build_standard( - data_manager_input, + data_manager_output, kraken2_args, target_directory, ) - open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input)) + open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) if __name__ == "__main__":
--- a/data_manager_conf.xml Mon Mar 04 19:24:23 2019 -0500 +++ b/data_manager_conf.xml Mon Mar 04 20:09:07 2019 -0500 @@ -5,11 +5,11 @@ <column name="value"/> <column name="name"/> <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases</target> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases</value_translation> - <value_translation type="function">abspath</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> </column> </output> </data_table> @@ -20,11 +20,11 @@ <column name="value"/> <column name="name"/> <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases</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_databases</value_translation> - <value_translation type="function">abspath</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> </column> </output> </data_table> @@ -35,11 +35,11 @@ <column name="value"/> <column name="name"/> <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases</target> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases</value_translation> - <value_translation type="function">abspath</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> </column> </output> </data_table>