Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 3:b03007bc0f05 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
| author | dfornika |
|---|---|
| date | Thu, 28 Feb 2019 18:55:04 -0500 |
| parents | cf0cda80b659 |
| children | 988c436ad798 |
| files | data_manager/kraken2_build_custom.py data_manager_conf.xml |
| diffstat | 2 files changed, 16 insertions(+), 0 deletions(-) [+] |
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--- a/data_manager/kraken2_build_custom.py Thu Feb 28 18:18:01 2019 -0500 +++ b/data_manager/kraken2_build_custom.py Thu Feb 28 18:55:04 2019 -0500 @@ -76,6 +76,7 @@ parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) + parser.add_argument( '-f', '--fasta', dest='fasta', help='fasta' ) parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) args = parser.parse_args()
--- a/data_manager_conf.xml Thu Feb 28 18:18:01 2019 -0500 +++ b/data_manager_conf.xml Thu Feb 28 18:55:04 2019 -0500 @@ -44,4 +44,19 @@ </output> </data_table> </data_manager> + <data_manager tool_file="data_manager/kraken2_build_custom.xml" id="kraken2_build_custom" 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_managers>