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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
author iuc
date Thu, 24 Oct 2024 18:10:50 +0000
parents 462e62be07e1
children
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462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
1 VARVAMP log
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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2
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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3 MODE = qpcr
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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4
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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5
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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6 ARG SETTINGS
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
7
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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8 THRESHOLD = 0.7
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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9 PRIMER_ALLOWED_N_AMB = 1
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
10 PROBE_ALLOWED_N_AMB = 1
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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11 TEST_DELTAG_N_AMPLICONS = 180
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
12 DELTAG_CUTOFF = -15
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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13
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
14 CONFIG SETTINGS
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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15
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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16 PRIMER_TMP = (56, 63, 60)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
17 PRIMER_GC_RANGE = (35, 65, 50)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
18 PRIMER_SIZES = (18, 24, 21)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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19 PRIMER_HAIRPIN = 47
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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20 PRIMER_MAX_POLYX = 4
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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21 PRIMER_MAX_DINUC_REPEATS = 4
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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22 PRIMER_GC_END = (1, 3)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
23 PRIMER_MAX_DIMER_TMP = 47
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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24 PRIMER_MIN_3_WITHOUT_AMB = 3
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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25 PCR_MV_CONC = 100
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
26 PCR_DV_CONC = 2
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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27 PCR_DNTP_CONC = 0.8
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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28 PCR_DNA_CONC = 15
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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29 PRIMER_TM_PENALTY = 2
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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30 PRIMER_GC_PENALTY = 0.2
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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31 PRIMER_SIZE_PENALTY = 0.5
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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32 PRIMER_MAX_BASE_PENALTY = 10
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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34 PRIMER_PERMUTATION_PENALTY = 0.1
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
35 QPROBE_TMP = (64, 70, 67)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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36 QPROBE_SIZES = (20, 30, 25)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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37 QPROBE_GC_RANGE = (40, 80, 60)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
38 QPROBE_GC_END = (0, 4)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
39 QPRIMER_DIFF = 2
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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40 QPROBE_TEMP_DIFF = (5, 10)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
41 QPROBE_DISTANCE = (4, 15)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
42 QAMPLICON_LENGTH = (70, 200)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff changeset
43 QAMPLICON_GC = (40, 60)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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44 QAMPLICON_DEL_CUTOFF = 4
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
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45