Mercurial > repos > devteam > lastz
comparison test-data/lastz_d_ctrl_file.txt @ 2:8e9252994649 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
| author | iuc |
|---|---|
| date | Fri, 02 Mar 2018 12:06:35 -0500 |
| parents | |
| children |
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| 1:3c13c9c09ad9 | 2:8e9252994649 |
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| 1 # base the inference on alignments in the middle half by identity | |
| 2 min_identity = 25.0% # 25th percentile | |
| 3 max_identity = 75.0% # 75th percentile | |
| 4 | |
| 5 # scale scores so max substitution score will be 100, and only use | |
| 6 # alignments scoring at least as well as 20 ideal matches | |
| 7 inference_scale = 100 # max substitution score | |
| 8 hsp_threshold = 20*inference_scale | |
| 9 gapped_threshold = hsp_threshold | |
| 10 | |
| 11 # allow substitution score inference to iterate at most 20 times; | |
| 12 # don't perform gap penalty inference -- instead hardwire gap penalties | |
| 13 # relative to max substitution | |
| 14 max_sub_iterations = 20 | |
| 15 max_gap_iterations = 0 | |
| 16 gap_open_penalty = 4*inference_scale | |
| 17 gap_extend_penalty = 0.3*inference_scale | |
| 18 | |
| 19 # use all seedword positions (don't sample) | |
| 20 step = 1 | |
| 21 | |
| 22 # adjust for entropy when qualifying HSPs | |
| 23 entropy = on |