Mercurial > repos > iuc > codeml

comparison test-data/1_codeml.ctl @ 1:ba71e26d5bdc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
author iuc
date Wed, 02 May 2018 05:44:08 -0400
parents 961a712f9743
children f9cb3a4339c2
comparison
equal deleted inserted replaced
0:961a712f9743 1:ba71e26d5bdc
1 1
2 seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_1.dat * sequence data file name 2 seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_1.dat * sequence data file name
3 outfile = run_codeml * main result file name 3 outfile = run_codeml * main result file name
4 treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_2.dat * tree structure file name 4 treefile = /tmp/tmpr0j4bmyj/files/000/dataset_2.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
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
44
45 44