Mercurial > repos > iuc > varvamp

comparison test-data/test3.log @ 2:baa1589657e1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp commit 7a60f4dbf7aecdc394570a48009e3283e4d83745
author iuc
date Thu, 05 Feb 2026 18:00:21 +0000
parents 7a586a157d37
children
comparison
equal deleted inserted replaced
1:209d074eb024 2:baa1589657e1
1 VARVAMP log 1 VARVAMP log
2 2
3 MODE = qpcr 3 MODE = qpcr
4 4
5 5
6 ARG SETTINGS 6 ARG SETTINGS
7 7
8 THRESHOLD = 0.7 8 THRESHOLD = 0.7
9 PRIMER_ALLOWED_N_AMB = 1 9 PRIMER_ALLOWED_N_AMB = 1
10 PROBE_ALLOWED_N_AMB = 1 10 PROBE_ALLOWED_N_AMB = 1
11 TEST_DELTAG_N_AMPLICONS = 180 11 TEST_DELTAG_N_AMPLICONS = 10
12 DELTAG_CUTOFF = -15 12 DELTAG_CUTOFF = -15
13 13
14 CONFIG SETTINGS 14 CONFIG SETTINGS
15 15
16 PRIMER_TMP = (56, 63, 60) 16 PRIMER_TMP = (56, 63, 60)
18 PRIMER_SIZES = (18, 24, 21) 18 PRIMER_SIZES = (18, 24, 21)
19 PRIMER_HAIRPIN = 47 19 PRIMER_HAIRPIN = 47
20 PRIMER_MAX_POLYX = 4 20 PRIMER_MAX_POLYX = 4
21 PRIMER_MAX_DINUC_REPEATS = 4 21 PRIMER_MAX_DINUC_REPEATS = 4
22 PRIMER_GC_END = (1, 3) 22 PRIMER_GC_END = (1, 3)
23 PRIMER_MAX_DIMER_TMP = 47 23 PRIMER_MAX_DIMER_TMP = 35
24 PRIMER_MIN_3_WITHOUT_AMB = 3 24 PRIMER_MIN_3_WITHOUT_AMB = 3
25 PCR_MV_CONC = 100 25 PCR_MV_CONC = 100
26 PCR_DV_CONC = 2 26 PCR_DV_CONC = 2
27 PCR_DNTP_CONC = 0.8 27 PCR_DNTP_CONC = 0.8
28 PCR_DNA_CONC = 15 28 PCR_DNA_CONC = 15
30 PRIMER_GC_PENALTY = 0.2 30 PRIMER_GC_PENALTY = 0.2
31 PRIMER_SIZE_PENALTY = 0.5 31 PRIMER_SIZE_PENALTY = 0.5
32 PRIMER_MAX_BASE_PENALTY = 10 32 PRIMER_MAX_BASE_PENALTY = 10
33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2) 33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
34 PRIMER_PERMUTATION_PENALTY = 0.1 34 PRIMER_PERMUTATION_PENALTY = 0.1
35 END_OVERLAP = 5
35 QPROBE_TMP = (64, 70, 67) 36 QPROBE_TMP = (64, 70, 67)
36 QPROBE_SIZES = (20, 30, 25) 37 QPROBE_SIZES = (20, 30, 25)
37 QPROBE_GC_RANGE = (40, 80, 60) 38 QPROBE_GC_RANGE = (40, 80, 60)
38 QPROBE_GC_END = (0, 4) 39 QPROBE_GC_END = (0, 4)
39 QPRIMER_DIFF = 2 40 QPRIMER_DIFF = 2
40 QPROBE_TEMP_DIFF = (5, 10) 41 QPROBE_TEMP_DIFF = (5, 10)
41 QPROBE_DISTANCE = (4, 15) 42 QPROBE_DISTANCE = (4, 15)
42 QAMPLICON_LENGTH = (70, 200) 43 QAMPLICON_LENGTH = (70, 200)
43 QAMPLICON_GC = (40, 60) 44 QAMPLICON_GC = (40, 60)
44 QAMPLICON_DEL_CUTOFF = 4 45 QAMPLICON_DEL_CUTOFF = 4
45