Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
changeset 8:cbe62bd6e149 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Tue, 23 Jul 2019 11:12:15 -0400 |
| parents | 954d617c323d |
| children | 9004217cddf4 |
| files | data_manager/salmon_index_builder.py data_manager/salmon_index_builder.xml data_manager_conf.xml |
| diffstat | 3 files changed, 3 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager/salmon_index_builder.py Tue Jul 23 10:50:43 2019 -0400 +++ b/data_manager/salmon_index_builder.py Tue Jul 23 11:12:15 2019 -0400 @@ -59,6 +59,7 @@ parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes' ) + parser.add_argument( '-v','--index_version', dest='index_version', action='store', type=str, help='Use IndexVersion attribute from header.json' ) parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' ) options = parser.parse_args()
--- a/data_manager/salmon_index_builder.xml Tue Jul 23 10:50:43 2019 -0400 +++ b/data_manager/salmon_index_builder.xml Tue Jul 23 11:12:15 2019 -0400 @@ -12,7 +12,7 @@ --fasta_dbkey '${all_fasta_source.fields.dbkey}' --fasta_description '${all_fasta_source.fields.name}' --kmer_size "${kmer_size}" - --data_table_name salmon_indexes + --data_table_name salmon_indexes_versioned --index_version @IDX_VERSION@ ]]> </command>
--- a/data_manager_conf.xml Tue Jul 23 10:50:43 2019 -0400 +++ b/data_manager_conf.xml Tue Jul 23 11:12:15 2019 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/salmon_index_builder.xml" id="salmon_index_builder" version="0.1"> - <data_table name="salmon_indexes"> + <data_table name="salmon_indexes_versioned"> <output> <column name="value" /> <column name="dbkey" />