codeml: codeml.xml annotate

annotate codeml.xml @ 4:682e5eca7458 draft default tip

"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	96806adbb000
children

rev	line source
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	1 <tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy2" profile="18.01">
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	2 <description>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	3 Detects positive selection (paml package)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	4 </description>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	5
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	6 <macros>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	7 <import>macros.xml</import>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	8 </macros>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	9
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	10 <requirements>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">paml</requirement>
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	12 </requirements>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	13
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	14 <version_command><![CDATA[ codeml /dev/null 2>&1 \| tail -1 ]]></version_command>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	15
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	16 <command><![CDATA[
2 853e3ce30204 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 29dba85647adf75fd7276d5da0f3cc1b8eda23ea" iuc parents: 1 diff changeset	17 cp '$codeml_ctl' '$ctl' &&
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	18 codeml '$codeml_ctl'
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	19 ]]></command>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	20
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	21 <configfiles>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	22 <configfile name="codeml_ctl"><![CDATA[
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	23 seqfile = $concat_nuc * sequence data file name
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	24 outfile = run_codeml * main result file name
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	25 treefile = $tree * tree structure file name
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	26 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	27 verbose = $adv.verbose * 1: detailed output, 0: concise output
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	28 runmode = $adv.runmode * 0: user tree; 1: semi-automatic; 2: automatic
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	29 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	30 seqtype = $adv.seqtype * 1:codons; 2:AAs; 3:codons-->AAs
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	31 CodonFreq = $adv.CodonFreq * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	32 clock = $adv.clock * 0:no clock, 1:clock; 2:local clock
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	33 aaDist = $adv.aaDist * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	34 * 7:AAClasses
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	35 aaRatefile = $adv.aaRateFile * only used for aa seqs with model=empirical(_F)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	36 * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	37 model = $compat_model.brmodel
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	38 * models for codons:
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	39 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	40 * models for AAs or codon-translated AAs:
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	41 * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	42 * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	43 NSsites = $compat_model.NSsites * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	44 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	45 * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	46 * 13:3normal>0
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	47 icode = $adv.icode * 0:universal code; 1:mammalian mt; 2-11:see below
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	48 Mgene = $adv.Mgene * 0:rates, 1:separate;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	49 fix_kappa = $adv.fix_kappa * 1: kappa fixed, 0: kappa to be estimated
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	50 kappa = $adv.kappa * initial or fixed kappa
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	51 fix_omega = $adv.fix_omega * 1: omega or omega_1 fixed, 0: estimate
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	52 omega = $adv.omega * initial or fixed omega, for codons or codon-based AAs
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	53 fix_alpha = $adv.fix_alpha * 0: estimate gamma shape parameter; 1: fix it at alpha
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	54 alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	55 Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	56 ncatG = $adv.ncatG * # of categories in dG of NSsites models
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	57 fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	58 rho = $adv.rho * initial or fixed rho, 0:no correlation
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	59 getSE = $adv.getSE * 0: dont want them, 1: want S.E.s of estimates
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	60 RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	61 Small_Diff = $adv.Small_Diff
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	62 cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)?
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	63 fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	64 method = $adv.method * 0: simultaneous; 1: one branch at a time
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	65 ]]></configfile>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	66 </configfiles>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	67
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	68 <inputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	69 <param name="concat_nuc" type="data" format="fasta" label="Sequences file" help="The fasta file with the sequences to be analyzed" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	70 <param name="tree" type="data" format="nhx" label="tree file" help="Tree file in Newick format" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	71
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	72 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	73 <param argument="brmodel" type="select" label="Branch model ; for tree file editing in model 2 and 3, see paml manual (chap.3)" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	74 <option value="0" selected="true">'0' : one dN/dS ratio for all branches (e.g. basic model if NSsites=0)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	75 <option value="1">'1' : one dN/dS ratio for each branch ("free-ratio model") ; its use is discouraged</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	76 <option value="2">'2' : arbitrary number of ratios ; implies to manually edit your tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	77 <option value="3">'3' : clade-model ; implies to manually edit your tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	78 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	79
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	80 <when value="0" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	81 <expand macro="FSsites_br0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	82 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	83 <when value="1">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	84 <expand macro="FSsites_br1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	85 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	86 <when value="2" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	87 <expand macro="FSsites_br2_and_3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	88 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	89 <when value="3" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	90 <expand macro="FSsites_br2_and_3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	91 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	92 </conditional>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	93
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	94 <!-- advanced parameters -->
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	95 <section name="adv" title="Advanced Options" expanded="False" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	96 <param argument="verbose" type="select" label="Set the level of details in the log file">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	97 <option value="0" selected="true">0 : concise output</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	98 <option value="1">1 : detailed output</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	99 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	100
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	101 <param argument="runmode" type="select" label="Tree analysis mode" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	102 <option value="0" selected="true">0 : user tree</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	103 <option value="1">1 : heuristic tree search starting from a multifurcating tree from the tree structure file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	104 <option value="2">2 : heuristic tree search starting from the tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	105 <option value="3">3 : StepwiseAddition</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	106 <option value="4">4 : PerturbationNNI with the starting tree obtained by a parsimony algorithm</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	107 <option value="5">5 : PerturbationNNI with the starting tree read from the tree structure file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	108 <option value="-2">-2 : ML estimation of dS and dN in pairwise comparisons of protein-coding sequences</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	109 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	110
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	111 <param argument="seqtype" type="select" label="Sequences format in the fasta file" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	112 <option value="1" selected="true">1 : codons</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	113 <option value="2">2 : Amino acids (only compatible with FSsites=0) </option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	114 <option value="3">3 : codons-->amino acids (only compatible with FSsites=0)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	115 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	116
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	117 <param argument="CodonFreq" type="select" label="Equilibrium codon frequencies in codon substitution model">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	118 <option value="0">0 : 1/61 each:</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	119 <option value="1" selected="true">1 : FIX4</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	120 <option value="2">2 : codon table</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	121 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	122
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	123 <param argument="clock" type="select" label="Specifies models concerning rate constancy or variation among lineages" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	124 <option value="0" selected="true">0 : no clock ; An unrooted tree should be used under this model</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	125 <option value="1">1 : clock</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	126 <option value="2">2 : local clock (needed : branch labels in the tree)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	127 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	128
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	129 <param argument="aaDist" type="select" label="Amino acid distances" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	130 <option value="0" selected="true">0 : equal (warning : the only one compatible with NSsites and seqtype=codons</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	131 <option value="+">+ : geometric</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	132 <option value="-">- : linear</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	133 <option value="1">1 : G1974</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	134 <option value="2">2 : Miyata</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	135 <option value="3">3 : c</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	136 <option value="4">4 : p</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	137 <option value="5">5 : v</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	138 <option value="6">6 : a</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	139 <option value="7">7 : AAClasses</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	140 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	141
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	142 <param argument="aaRateFile" type="select" label="Amino acide substitution rate matrix" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	143 <option value="wag.dat" selected="true">wag.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	144 <option value="dayhoff.dat">dayhoff.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	145 <option value="jones.dat">jones.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	146 <option value="mtmam.dat">mtmam.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	147 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	148
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	149 <param argument="icode" type="select" label="Icode : specifies the genetic code" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	150 <option value="0" selected="true">0 : universal code</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	151 <option value="1">1 : mammalian mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	152 <option value="3">3 : mold mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	153 <option value="4">4 : invertebrate mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	154 <option value="5">5 : ciliate nuclear code mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	155 <option value="6">6 : echinoderm mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	156 <option value="7">7 : euplotid mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	157 <option value="8">8 : alternative yeast nuclear</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	158 <option value="9">9 : scidian mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	159 <option value="10">10 : blepharisma nuclear</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	160 <option value="11">11 : Yang's regularized code</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	161 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	162
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	163 <param argument="Mgene" type="select" value="0" label="Multiple genes"
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	164 help="Used in combination with option G in the sequence data file, for combined analysis of data from multiple genes or multiple site partitions" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	165 <option value="0">0 : complete homogeneity among genes </option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	166 <option value="1">1 : equivalent to a separate analysis</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	167 <option value="2">2 : different frequency parameters for different genes but the same rate ratio parameters</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	168 <option value="3">3 : different rate ratio parameters and the same frequency parameters</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	169 <option value="4">4 : both different rate ratio parameters and different frequency parameters for different genes </option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	170 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	171
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	172 <param argument="fix_kappa" type="select" label="Specifies wether kappa in K80, F84, or HKY85 is fixed or estimated">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	173 <option value="0" selected="true">0 : estimated</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	174 <option value="1">1 : fixed (the next parameter below)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	175 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	176
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	177 <param argument="kappa" type="float" value="2" label="Initial or fixed value of kappa" help="kappa refers to the transition/tranversion rate ratio"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	178
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	179 <param argument="fix_omega" type="select" label="Fixed or estimated omega" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	180 <option value="0" selected="true">0 : estimated</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	181 <option value="1">1 : fixed</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	182 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	183
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	184 <param argument="omega" type="float" value="0.2" label="Initial or fixed omega (according to your choice for fix_omega), for codons or codon-based AAs"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	185
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	186 <param argument="fix_alpha" type="select" label="Estimated or fixed gamma shape parameter" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	187 <option value="0">0 : estimate gamma shape parameter. Not recommended</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	188 <option value="1" selected="true">1 : fix it at alpha (the next parameter below)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	189 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	190
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	191 <param argument="alpha" type="float" value="0" label="Initial or fixed value of alpha (gamma shape parameter)"
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	192 help="0: constant rate. fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	193
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	194 <param argument="Malpha" type="select" label="Different alphas for genes" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	195 <option value="0">0 : one gamma distribution will be applied across all sites (one alpha)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	196 <option value="1">1 : different gamma distribution is used for each gene or codon position (different alphas for genes)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	197 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	198
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	199 <param argument="ncatG" type="integer" value="3" label="# of categories in dG of NSsites models" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	200
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	201 <param argument="fix_rho" type="select" label="Independence or correlation of rates at adjacent sites" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	202 <option value="0">0 : estimate rho</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	203 <option value="1" selected="true">1 : fix it at rho (the next parameter below)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	204 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	205
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	206 <param argument="rho" type="float" value="0" label="Initial or fixed rho" help="fix_rho=1 and rho=0 : independent rates" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	207
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	208 <param argument="getSE" type="select" label="Estimates of the standard errors of estimated parameters." >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	209 <option value="0" selected="true">0 : don't want them</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	210 <option value="1">1 : want S.E.s of estimates</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	211 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	212
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	213 <param argument="RateAncestor" type="select" label="RateAncestor ; set 1 to force the program to do two additional analyses" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	214 <option value="0" selected="true">0 : usually use 0</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	215 <option value="1">1 : model of variable rates across site + empirical Bayesian reconstruction of ancestral sequences</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	216 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	217
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	218 <param argument="Small_Diff" type="float" value=".5e-6" label="Value used in the difference approximation of derivatives"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	219
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	220 <param argument="cleandata" type="select" label="Remove sites with ambiguity data" help="Warning : choosing 'yes' may remove a lot (possibly all) of data.">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	221 <option value="0" selected="true">0 : no (don't remove ambiguous data)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	222 <option value="1">1 : yes (remove ambiguous data)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	223 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	224
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	225 <param argument="fix_blength" type="select" label="branch length dealing" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	226 <option value="0" selected="true">0 : ignore branch lengths</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	227 <option value="-1">-1 : start from random starting points</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	228 <option value="1">1 : initial values as written in the tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	229 <option value="2">2 : fixed at values in the tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	230 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	231
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	232 <param argument="method" type="select" label="Controls the iteration algorithm for estimating branch lengths" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	233 <option value="0" selected="true">0 : simultaneous (old paml algorithm)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	234 <option value="1">1 : one branch at a time (newly implemented in paml ; does not work with clock=1,2,3)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	235 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	236 </section>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	237 </inputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	238
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	239 <outputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	240 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	241 <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	242 <filter>adv['seqtype']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	243 </data>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	244 <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	245 <filter>adv['seqtype']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	246 </data>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	247 <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	248 <filter>adv['seqtype']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	249 </data>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	250 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	251 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	252 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	253 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	254 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	255 <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	256 <filter>adv['verbose']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	257 </data>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	258 </outputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	259
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	260 <tests>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	261 <test expect_num_outputs="9">
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	262 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	263 <param name="brmodel" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	264 <param name="NSsites" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	265 </conditional>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	266 <param name="adv\|fix_omega" value="0" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	267 <param name="adv\|omega" value="0.2" />
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	268 <param name="RateAncestor" value="1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	269 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	270 <param name="tree" value="RAxML_bestTree" ftype="nhx" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	271 <output name="twongdn" value="1_2ngdn" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	272 <output name="twongds" value="1_2ngds" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	273 <output name="twongt" value="1_2ngt" />
3 96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	274 <output name="run">
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	275 <assert_contents>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	276 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	277 <has_text text="Time used:" />
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	278 </assert_contents>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	279 </output>
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	280 <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	281 </test>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	282 <test expect_num_outputs="9">
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	283 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	284 <param name="brmodel" value="2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	285 <param name="NSsites" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	286 </conditional>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	287 <param name="adv\|fix_omega" value="0" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	288 <param name="adv\|omega" value="0.2" />
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	289 <param name="RateAncestor" value="1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	290 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	291 <param name="tree" value="tree_model2" ftype="nhx" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	292 <output name="twongdn" value="2_2ngdn" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	293 <output name="twongds" value="2_2ngds" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	294 <output name="twongt" value="2_2ngt" />
3 96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	295 <output name="run">
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	296 <assert_contents>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	297 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	298 <has_text text="Time used:" />
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	299 </assert_contents>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	300 </output>
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	301 <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	302 </test>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	303 <test expect_num_outputs="9">
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	304 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	305 <param name="brmodel" value="3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	306 <param name="NSsites" value="2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	307 </conditional>
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	308 <param name="adv\|fix_omega" value="0" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	309 <param name="adv\|omega" value="0.2" />
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	310 <param name="RateAncestor" value="1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	311 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4 682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	312 <param name="tree" value="tree_model3" ftype="nhx" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	313 <output name="twongdn" value="3_2ngdn" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	314 <output name="twongds" value="3_2ngds" />
682e5eca7458 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	315 <output name="twongt" value="3_2ngt" />
3 96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	316 <output name="run">
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	317 <assert_contents>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	318 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	319 <has_text text="Time used:" />
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	320 </assert_contents>
96806adbb000 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	321 </output>
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	322 <output name="ctl" value="3_codeml.ctl" lines_diff="4" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	323 </test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	324 </tests>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	325
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	326 <help><![CDATA[
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	327 .. class:: infomark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	328
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	329 Galaxy integration Victor Mataigne and ABIMS TEAM.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	330
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	331 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	332
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	333 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	334
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	335 CompCodeML (from paml package)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	336
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	337 A few help is detailed below ; full and detailed codeml readme can be found on the paml website_.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	338
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	339 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	340
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	341 .. class:: warningmark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	342
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	343 Due to their high number, some parameters incompatibility can remain.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	344
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	345 This Galaxy implementation :
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	346
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	347 - handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	348 - warns the user in a help section when an advanced parameter has known incompatibilities (the tool CAN be run, but the output files will be empty).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	349
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	350 We recommand to have a look at the full paml manual before looking at the advanced parameters, in order to spot parameters incompatibilities and to know what each model does. If you choose by mistake incompatible parameters, the output files will be empty, except the log file ("run_codeml" output) which will normally explicit the error.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	351
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	352 .. class:: infomark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	353
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	354 Known incompatibilities:
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	355
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	356 - 'seqtype' = 3 : only compatible with 'FSsites' = 0.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	357 - 'clock' = 2 : needs branch labels in the tree.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	358 - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	359 - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	360 - 'method' = 1 : does not work with 'clock' different than 0.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	361
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	362 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	363
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	364 Description
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	365
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	366 .. class:: infomark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	367
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	368 codeML finds positive selection within branches or codons within a tree and a set of sequences.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	369
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	370 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	371
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	372 Input files
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	373
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	374 - a treefile in Newick format (with or without branch lengths).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	375 - a fasta file with sequences from the species of the tree file (one header/sequence per species) and run codeml (from the paml suite).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	376
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	377 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	378
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	379 Parameters
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	380
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	381 Several models are available.
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	382
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	383 - branch models ("model" parameter).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	384 - sites models ("NSsites" parameter, model is left at 0).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	385 - branch-sites models (when model = 2 NSsites=2,3).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	386 - Clade models (when model=3 NSsites=2,3).
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	387
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	388 Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	389
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	390 .. class:: infomark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	391
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	392 Branch models allow the omega ratio to vary among branches in the phylogeny and are useful for detecting positive selection acting on particular lineages. Sites models allow the omega ratio to vary among sites (codons or amino acids).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	393
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	394 Two pairs of models appear to be particularly useful, forming two likelihood ratio tests of positive selection. The first compares M1a ('NearlyNeutral', NSsites=1) and M2a ('PositiveSelection', NSsites=2), while the second compares M7 ('beta', NSsites=7) and M8 ('beta&ω', NSsites=8).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	395
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	396 Other examples of model
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	397
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	398 How to run the branch-site models (A & B in Yang & Nielsen 2002 MBE) ?
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	399 The options are :
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	400
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	401 - Model A: (model=2, NSsites=2).
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	402 - Model B: (model=2, NSsites=3).
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	403
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	404 How to run the M0 (one-ratio) model :
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	405
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	406 model = 0, NSsites= = 0.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	407
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	408 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	409
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	410 Advanced Parameters
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	411
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	412 .. class:: infomark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	413
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	414 See paml complete manual and FAQ on the paml website_.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	415
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	416 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	417
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	418 Details of some parameters :
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	419
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	420 - 'kappa' denotes the transition/transversion rate ratio.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	421 - 'fix_kappa' specifies whether kappa in K80, F84, or HKY85 is given at a fixed value or is to be estimated by iteration from the data.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	422
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	423 -> If fix_kappa = 1 (fixed), the value of kappa is the given value
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	424
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	425 -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	426
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	427 - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	428 - 'fix_alpha' works in a similar way that fix_kappa.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	429
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	430 -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	431
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	432 -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	433
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	434 - fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995).
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	435
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	436 -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	437
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	438 -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	439
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	440 -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	441
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	442 -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	443
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	444 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	445
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	446 Output files
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	447
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	448 - codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	449 - run_codeml : main result file name.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	450 - The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	451 - lnf, rst and rst1: Supplemental results.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	452 - rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood).
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	453
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	454 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	455
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	456 How to edit manually the tree file : Branch or node labels
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	457
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	458 Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	459
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	460 - For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	461 - Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models.
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	462 - All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified.
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	463
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	464 In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	465 The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	466
1 5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	467 The following trees are equivalent:
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	468 - ((rabbit, rat) $1, human), goat_cow, marsupial);
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	469 - (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
0 6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	470
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	471 $ is the symbol for clade labels.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	472
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	473 Rules concerning nested clade labels : The symbol # takes precedence over the symbol $, and clade labels close to the tips take precedence over clade labels for ancestral nodes close to the root.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	474
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	475 In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	476 $1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	477 Equivalent tree with only '#' :
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	478 ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	479 ]]></help>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	480
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	481 <citations>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	482 <citation type="doi">10.1093/molbev/msm088</citation>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	483 </citations>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	484 </tool>

Mercurial > repos > iuc > codeml

annotate codeml.xml @ 4:682e5eca7458 draft default tip