Mercurial > repos > iuc > codeml

comparison test-data/3_codeml.ctl @ 4:f9cb3a4339c2 draft

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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 09:55:34 +0000
parents ba71e26d5bdc
children
comparison
equal deleted inserted replaced
3:b2b8e75a962d 4:f9cb3a4339c2
1 1
2 seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_23.dat * sequence data file name 2 seqfile = /tmp/tmpag83k3gw/files/9/9/6/dataset_99661b4e-1dc8-471d-9db3-6eb3d2655fbe.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_24.dat * tree structure file name 4 treefile = /tmp/tmpag83k3gw/files/d/4/d/dataset_d4d2b602-4042-48d7-9636-abdf169513fa.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