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comparison test-data/2_codeml.ctl @ 4:682e5eca7458 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
author iuc
date Sat, 27 Nov 2021 09:54:56 +0000
parents 5750c1f4b0eb
children
comparison
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3:96806adbb000 4:682e5eca7458
1 1
2 seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_12.dat * sequence data file name 2 seqfile = /tmp/tmpag83k3gw/files/2/6/2/dataset_262fd0d9-9018-4668-992c-0ed4943f9168.dat * sequence data file name
3 outfile = run_codeml * main result file name 3 outfile = run_codeml * main result file name
4 treefile = /tmp/tmpr0j4bmyj/files/000/dataset_13.dat * tree structure file name 4 treefile = /tmp/tmpag83k3gw/files/c/2/b/dataset_c2b7d4a1-033d-4bd9-92ba-ad7936f0c09a.dat * tree structure file name
5 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 5 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
6 verbose = 0 * 1: detailed output, 0: concise output 6 verbose = 0 * 1: detailed output, 0: concise output
7 runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 7 runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
8 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise 8 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
9 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 9 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
33 alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate) 33 alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate)
34 Malpha = 0 * 1: different alphas for genes, 0 : one alpha 34 Malpha = 0 * 1: different alphas for genes, 0 : one alpha
35 ncatG = 3 * # of categories in dG of NSsites models 35 ncatG = 3 * # of categories in dG of NSsites models
36 fix_rho = 1 * 0: estimate rho; 1: fix it at rho 36 fix_rho = 1 * 0: estimate rho; 1: fix it at rho
37 rho = 0.0 * initial or fixed rho, 0:no correlation 37 rho = 0.0 * initial or fixed rho, 0:no correlation
38 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 38 getSE = 0 * 0: dont want them, 1: want S.E.s of estimates
39 RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) 39 RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
40 Small_Diff = 5e-07 40 Small_Diff = 5e-07
41 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? 41 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
42 fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 42 fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
43 method = 0 * 0: simultaneous; 1: one branch at a time 43 method = 0 * 0: simultaneous; 1: one branch at a time