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comparison test-data/fastqc_customlimits.txt @ 18:7d3cef9c42ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 89976e27bd11f1da3c95a5df6b67297496a8a89b
author iuc
date Thu, 16 May 2019 07:45:20 -0400
parents 7b0207bd2183
children
comparison
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17:7b0207bd2183 18:7d3cef9c42ca
1 # For each of the modules you can choose to not run that 1 # For each of the modules you can choose to not run that
2 # module at all by setting the value below to 1 for the 2 # module at all by setting the value below to 1 for the
3 # modules you want to remove. 3 # modules you want to remove.
4 duplication ignore 1 4 duplication ignore 0
5 kmer ignore 0 5 kmer ignore 0
6 n_content ignore 0 6 n_content ignore 0
7 overrepresented ignore 0 7 overrepresented ignore 0
8 quality_base ignore 0 8 quality_base ignore 0
9 sequence ignore 0 9 sequence ignore 0
10 gc_sequence ignore 0 10 gc_sequence ignore 0
11 quality_sequence ignore 1 11 quality_sequence ignore 0
12 tile ignore 1 12 tile ignore 0
13 sequence_length ignore 0 13 sequence_length ignore 0
14 adapter ignore 0 14 adapter ignore 0
15 15
16 # For the duplication module the value is the percentage 16 # For the duplication module the value is the percentage
17 # remaining after deduplication. Measured levels below 17 # remaining after deduplication. Measured levels below
32 32
33 # For the overrepresented seqs the warn value sets the 33 # For the overrepresented seqs the warn value sets the
34 # threshold for the overrepresented sequences to be reported 34 # threshold for the overrepresented sequences to be reported
35 # at all as the proportion of the library which must be seen 35 # at all as the proportion of the library which must be seen
36 # as a single sequence 36 # as a single sequence
37 overrepresented warn 0.001 37 overrepresented warn 0.1
38 overrepresented error 1 38 overrepresented error 1
39 39
40 # The per base quality filter uses two values, one for the value 40 # The per base quality filter uses two values, one for the value
41 # of the lower quartile, and the other for the value of the 41 # of the lower quartile, and the other for the value of the
42 # median quality. Failing either of these will trigger the alert 42 # median quality. Failing either of these will trigger the alert
43 quality_base_lower warn 10 43 quality_base_lower warn 10
44 quality_base_lower error 5 44 quality_base_lower error 5
45 quality_base_median warn 50 45 quality_base_median warn 25
46 quality_base_median error 20 46 quality_base_median error 20
47 47
48 # The per base sequence content module tests the maximum deviation 48 # The per base sequence content module tests the maximum deviation
49 # between A and T or C and G 49 # between A and T or C and G
50 sequence warn 2 50 sequence warn 10
51 sequence error 5 51 sequence error 20
52 52
53 # The per sequence GC content tests the maximum deviation between 53 # The per sequence GC content tests the maximum deviation between
54 # the theoretical distribution and the real distribution 54 # the theoretical distribution and the real distribution
55 gc_sequence warn 15 55 gc_sequence warn 15
56 gc_sequence error 30 56 gc_sequence error 30