Mercurial > repos > dfornika > mentalist
changeset 19:9a90295d0dfb draft
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty
| author | dfornika |
|---|---|
| date | Wed, 11 Oct 2017 18:01:26 -0400 |
| parents | c3cef07b5132 |
| children | 3738f0bc436b |
| files | data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py tools/mentalist_call/mentalist_call.xml |
| diffstat | 3 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Wed Oct 11 17:49:06 2017 -0400 +++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Wed Oct 11 18:01:26 2017 -0400 @@ -26,7 +26,7 @@ if return_code: print("Error building database.", file=sys.stderr) sys.exit( return_code ) - data_table_entry = dict( value=database_name, dbkey='cgMLST', name=display_name, path=database_path ) + data_table_entry = dict( value=database_name, dbkey='cgMLST', name=display_name, path=(database_path + "/" + database_name) ) for data_table_name in data_table_names: _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Wed Oct 11 17:49:06 2017 -0400 +++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Wed Oct 11 18:01:26 2017 -0400 @@ -26,7 +26,7 @@ if return_code: print("Error building database.", file=sys.stderr) sys.exit( return_code ) - data_table_entry = dict( value=database_name, dbkey='PubMLST', name=display_name, path=database_path ) + data_table_entry = dict( value=database_name, dbkey='PubMLST', name=display_name, path=(database_path + "/" + database_name) ) for data_table_name in data_table_names: _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
--- a/tools/mentalist_call/mentalist_call.xml Wed Oct 11 17:49:06 2017 -0400 +++ b/tools/mentalist_call/mentalist_call.xml Wed Oct 11 18:01:26 2017 -0400 @@ -7,7 +7,7 @@ call -o '$output_file' -s '$sample_name' - --db '$kmer_db.fields.path'/'$kmer_db.fields.value' + --db '$kmer_db.fields.path' #if $discard_threshold -t '$discard_threshold' #end if