annotate test-data/lastz_d_ctrl_file.txt @ 11:37b497aa133f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c
author iuc
date Sun, 02 Jul 2023 12:10:46 +0000
parents bd84ff27bc16
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bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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1 # base the inference on alignments in the middle half by identity
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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2 min_identity = 25.0% # 25th percentile
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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3 max_identity = 75.0% # 75th percentile
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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5 # scale scores so max substitution score will be 100, and only use
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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6 # alignments scoring at least as well as 20 ideal matches
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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7 inference_scale = 100 # max substitution score
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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8 hsp_threshold = 20*inference_scale
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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9 gapped_threshold = hsp_threshold
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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parents:
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bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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11 # allow substitution score inference to iterate at most 20 times;
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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12 # don't perform gap penalty inference -- instead hardwire gap penalties
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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13 # relative to max substitution
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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14 max_sub_iterations = 20
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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parents:
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15 max_gap_iterations = 0
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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parents:
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16 gap_open_penalty = 4*inference_scale
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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17 gap_extend_penalty = 0.3*inference_scale
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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19 # use all seedword positions (don't sample)
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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20 step = 1
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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22 # adjust for entropy when qualifying HSPs
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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23 entropy = on