Mercurial > repos > cstrittmatter > test_galtrakr_eurl_vtec_wgs_pt_23
changeset 4:d2a61d35af5d draft
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
| author | cstrittmatter |
|---|---|
| date | Tue, 21 Jan 2020 14:54:23 -0500 |
| parents | 55b65b497d49 |
| children | f739b302bc9a |
| files | EURL_VTEC_WGS_PT.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/EURL_VTEC_WGS_PT.py Tue Jan 21 12:00:36 2020 -0500 +++ b/EURL_VTEC_WGS_PT.py Tue Jan 21 14:54:23 2020 -0500 @@ -125,7 +125,7 @@ if os.stat('blastn_shigatoxin_fc').st_size == 0: os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct") # SEQUENCETYPER - os.system("mentalist call --output_votes -o 'mentalist_out' --db 'data/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_1.fq -2 input_2.fq") + os.system("mentalist call --output_votes -o 'mentalist_out' --db '/afs/galaxy/tool-data/mentalist_databases/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_1.fq -2 input_2.fq") os.system("mv mentalist_out.byvote " + args.mlstsevenloci) sequence_typing = openFileAsTable(args.mlstsevenloci) sequence_qc = openFileAsTable("mentalist_out.coverage.txt") @@ -213,7 +213,7 @@ if os.stat('blastn_shigatoxin_fc').st_size == 0: os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct") # SEQUENCETYPER - os.system("mentalist call --output_votes -o 'mentalist_out' --db 'data/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_1.fq") + os.system("mentalist call --output_votes -o 'mentalist_out' --db '/afs/galaxy/tool-data/mentalist_databases/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_1.fq") os.system("mv mentalist_out.byvote " + args.mlstsevenloci) sequence_typing = openFileAsTable(args.mlstsevenloci) sequence_qc = openFileAsTable("mentalist_out.coverage.txt")