# HG changeset patch
# User cstrittmatter
# Date 1579636463 18000
# Node ID d2a61d35af5d0360b0a00f3f080af1f06bf102b6
# Parent  55b65b497d491fe3873e8c4e24ea3d2882b762d6
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8

diff -r 55b65b497d49 -r d2a61d35af5d EURL_VTEC_WGS_PT.py
--- 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")