Mercurial > repos > dfornika > mentalist
changeset 73:31686a3c3018 draft default tip
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/mentalist_v0.1/galaxy commit 3510ff53b3c1cc42940733dfaa7036673c0cea2a
| author | dfornika |
|---|---|
| date | Wed, 03 Apr 2019 15:47:24 -0400 |
| parents | 7a90f3b437bf |
| children | |
| files | data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py |
| diffstat | 2 files changed, 3 insertions(+), 0 deletions(-) [+] |
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--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Tue Jun 26 13:27:00 2018 -0400 +++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Wed Apr 03 15:47:24 2019 -0400 @@ -20,6 +20,8 @@ <option value="Clostridioides difficile">Clostridioides difficile</option> <option value="Enterococcus faecium">Enterococcus faecium</option> <option value="Francisella tularensis">Francisella tularensis</option> + <option value="Klebsiella pneumoniae/variicola/quasipneumoniae">Klebsiella pneumoniae/variicola/quasipneumoniae</option> + <option value="Mycobacterium tuberculosis/bovis/africanum/canettii">Mycobacterium tuberculosis/bovis/africanum/canettii</option> <option value="Legionella pneumophila">Legionella pneumophila</option> <option value="Listeria monocytogenes">Listeria monocytogenes</option> <option value="Staphylococcus aureus">Staphylococcus aureus</option>
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Tue Jun 26 13:27:00 2018 -0400 +++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Wed Apr 03 15:47:24 2019 -0400 @@ -17,6 +17,7 @@ def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): + scheme = scheme.replace('__pd__','#') translation_table = string.maketrans(string.punctuation, ("_" * 32)) base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_pubmlst" today = datetime.date.today().isoformat()