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comparison test-data/test2.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 209d074eb024
children
comparison
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1:209d074eb024 2:baa1589657e1
1 VARVAMP log 1 VARVAMP log
2 2
3 MODE = tiled 3 MODE = tiled
4 4
5 WARNING: your amplicon lengths might be to small. Consider increasing 5 WARNING: your amplicon lengths might be to small. Consider increasing
6 WARNING: your intended overlap is higher than half of your optimal length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing. 6 WARNING: your min overlap is lower than your optimal length / 2 - 2 * min primer length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.
7 7
8 ARG SETTINGS 8 ARG SETTINGS
9 9
10 THRESHOLD = 0.6 10 THRESHOLD = 0.6
11 PRIMER_ALLOWED_N_AMB = 2 11 PRIMER_ALLOWED_N_AMB = 2
12 AMPLICON_OPT_LENGTH = 150 12 AMPLICON_OPT_LENGTH = 150
13 AMPLICON_MAX_LENGTH = 300 13 AMPLICON_MAX_LENGTH = 300
14 MIN_OVERLAP = 76 14 MIN_OVERLAP = 40
15 15
16 CONFIG SETTINGS 16 CONFIG SETTINGS
17 17
18 PRIMER_TMP = (56, 63, 60) 18 PRIMER_TMP = (56, 63, 60)
19 PRIMER_GC_RANGE = (35, 65, 50) 19 PRIMER_GC_RANGE = (35, 65, 50)
20 PRIMER_SIZES = (18, 24, 21) 20 PRIMER_SIZES = (18, 24, 21)
21 PRIMER_HAIRPIN = 47 21 PRIMER_HAIRPIN = 47
22 PRIMER_MAX_POLYX = 4 22 PRIMER_MAX_POLYX = 4
23 PRIMER_MAX_DINUC_REPEATS = 4 23 PRIMER_MAX_DINUC_REPEATS = 4
24 PRIMER_GC_END = (1, 3) 24 PRIMER_GC_END = (1, 3)
25 PRIMER_MAX_DIMER_TMP = 47 25 PRIMER_MAX_DIMER_TMP = 35
26 PRIMER_MIN_3_WITHOUT_AMB = 3 26 PRIMER_MIN_3_WITHOUT_AMB = 3
27 PCR_MV_CONC = 100 27 PCR_MV_CONC = 100
28 PCR_DV_CONC = 2 28 PCR_DV_CONC = 2
29 PCR_DNTP_CONC = 0.8 29 PCR_DNTP_CONC = 0.8
30 PCR_DNA_CONC = 15 30 PCR_DNA_CONC = 15
32 PRIMER_GC_PENALTY = 0.2 32 PRIMER_GC_PENALTY = 0.2
33 PRIMER_SIZE_PENALTY = 0.5 33 PRIMER_SIZE_PENALTY = 0.5
34 PRIMER_MAX_BASE_PENALTY = 10 34 PRIMER_MAX_BASE_PENALTY = 10
35 PRIMER_3_PENALTY = (32, 16, 8, 4, 2) 35 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
36 PRIMER_PERMUTATION_PENALTY = 0.1 36 PRIMER_PERMUTATION_PENALTY = 0.1
37 37 END_OVERLAP = 5