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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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
baa1589657e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp commit 7a60f4dbf7aecdc394570a48009e3283e4d83745
iuc
parents: 0
diff changeset
1 VARVAMP log
0
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
3 MODE = single
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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4
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
5
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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6 ARG SETTINGS
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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8 THRESHOLD = 0.8
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
9 PRIMER_ALLOWED_N_AMB = 3
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
10 AMPLICON_OPT_LENGTH = 300
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
11 AMPLICON_MAX_LENGTH = 400
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
12 REPORT_N_AMPLICONS = 5
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
14 CONFIG SETTINGS
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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15
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
16 PRIMER_TMP = (56, 63, 60)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
17 PRIMER_GC_RANGE = (35, 65, 50)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
18 PRIMER_SIZES = (18, 24, 21)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
19 PRIMER_HAIRPIN = 47
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
20 PRIMER_MAX_POLYX = 4
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
21 PRIMER_MAX_DINUC_REPEATS = 4
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
22 PRIMER_GC_END = (1, 3)
2
baa1589657e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp commit 7a60f4dbf7aecdc394570a48009e3283e4d83745
iuc
parents: 0
diff changeset
23 PRIMER_MAX_DIMER_TMP = 35
0
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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24 PRIMER_MIN_3_WITHOUT_AMB = 3
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
25 PCR_MV_CONC = 100
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
26 PCR_DV_CONC = 2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
27 PCR_DNTP_CONC = 0.8
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
28 PCR_DNA_CONC = 15
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
29 PRIMER_TM_PENALTY = 2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
30 PRIMER_GC_PENALTY = 0.2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
31 PRIMER_SIZE_PENALTY = 0.5
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
32 PRIMER_MAX_BASE_PENALTY = 10
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
diff changeset
33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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34 PRIMER_PERMUTATION_PENALTY = 0.1
2
baa1589657e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp commit 7a60f4dbf7aecdc394570a48009e3283e4d83745
iuc
parents: 0
diff changeset
35 END_OVERLAP = 5