Mercurial > repos > devteam > fastqc
comparison test-data/fastqc_customlimits.txt @ 18:3e1cdf5406db draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8a5d4f0470a7778a87d01dc84578f94a30ab7f43
| author | iuc |
|---|---|
| date | Mon, 05 Nov 2018 12:08:29 -0500 |
| parents | a00a6402d09a |
| children | 9da02be9c6cc |
comparison
equal
deleted
inserted
replaced
| 17:c15237684a01 | 18:3e1cdf5406db |
|---|---|
| 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 |