codeml: codeml.xml annotate

annotate codeml.xml @ 5:dba114391c98 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 866bfa31d035d511ca31f82c8ebac0f1df36b6ac

author	iuc
date	Fri, 09 Feb 2024 21:39:39 +0000
parents	f9cb3a4339c2
children

rev	line source
4 f9cb3a4339c2 "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 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	2 <description>
961a712f9743 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)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	4 </description>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	5 <macros>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	6 <import>macros.xml</import>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	7 </macros>
5 dba114391c98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 866bfa31d035d511ca31f82c8ebac0f1df36b6ac iuc parents: 4 diff changeset	8 <xrefs>
dba114391c98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 866bfa31d035d511ca31f82c8ebac0f1df36b6ac iuc parents: 4 diff changeset	9 <xref type="bio.tools">paml</xref>
dba114391c98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 866bfa31d035d511ca31f82c8ebac0f1df36b6ac iuc parents: 4 diff changeset	10 </xrefs>
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	11 <requirements>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	12 <requirement type="package" version="@TOOL_VERSION@">paml</requirement>
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	13 </requirements>
961a712f9743 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>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	15 <command><![CDATA[
2 66228e9c29d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 29dba85647adf75fd7276d5da0f3cc1b8eda23ea" iuc parents: 1 diff changeset	16 cp '$codeml_ctl' '$ctl' &&
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	17 codeml '$codeml_ctl'
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	18 ]]></command>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	19 <configfiles>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	20 <configfile name="codeml_ctl"><![CDATA[
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	21 seqfile = $concat_nuc * sequence data file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	22 outfile = run_codeml * main result file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	23 treefile = $tree * tree structure file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	24 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	25 verbose = $adv.verbose * 1: detailed output, 0: concise output
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	26 runmode = $adv.runmode * 0: user tree; 1: semi-automatic; 2: automatic
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	27 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	28 seqtype = $adv.seqtype * 1:codons; 2:AAs; 3:codons-->AAs
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	29 CodonFreq = $adv.CodonFreq * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	30 clock = $adv.clock * 0:no clock, 1:clock; 2:local clock
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	31 aaDist = $adv.aaDist * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	32 * 7:AAClasses
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	33 aaRatefile = $adv.aaRateFile * only used for aa seqs with model=empirical(_F)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	34 * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	35 model = $compat_model.brmodel
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	36 * models for codons:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	37 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	38 * models for AAs or codon-translated AAs:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	39 * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	40 * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	41 NSsites = $compat_model.NSsites * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	42 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	43 * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	44 * 13:3normal>0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	45 icode = $adv.icode * 0:universal code; 1:mammalian mt; 2-11:see below
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	46 Mgene = $adv.Mgene * 0:rates, 1:separate;
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	47 fix_kappa = $adv.fix_kappa * 1: kappa fixed, 0: kappa to be estimated
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	48 kappa = $adv.kappa * initial or fixed kappa
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	49 fix_omega = $adv.fix_omega * 1: omega or omega_1 fixed, 0: estimate
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	50 omega = $adv.omega * initial or fixed omega, for codons or codon-based AAs
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	51 fix_alpha = $adv.fix_alpha * 0: estimate gamma shape parameter; 1: fix it at alpha
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	52 alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	53 Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	54 ncatG = $adv.ncatG * # of categories in dG of NSsites models
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	55 fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	56 rho = $adv.rho * initial or fixed rho, 0:no correlation
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	57 getSE = $adv.getSE * 0: dont want them, 1: want S.E.s of estimates
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	58 RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	59 Small_Diff = $adv.Small_Diff
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	60 cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)?
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	61 fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	62 method = $adv.method * 0: simultaneous; 1: one branch at a time
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	63 ]]></configfile>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	64 </configfiles>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	65
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	66 <inputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	67 <param name="concat_nuc" type="data" format="fasta" label="Sequences file" help="The fasta file with the sequences to be analyzed" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	68 <param name="tree" type="data" format="nhx" label="tree file" help="Tree file in Newick format" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	69
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	70 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	71 <param argument="brmodel" type="select" label="Branch model ; for tree file editing in model 2 and 3, see paml manual (chap.3)" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	72 <option value="0" selected="true">'0' : one dN/dS ratio for all branches (e.g. basic model if NSsites=0)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	73 <option value="1">'1' : one dN/dS ratio for each branch ("free-ratio model") ; its use is discouraged</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	74 <option value="2">'2' : arbitrary number of ratios ; implies to manually edit your tree file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	75 <option value="3">'3' : clade-model ; implies to manually edit your tree file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	76 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	77
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	78 <when value="0" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	79 <expand macro="FSsites_br0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	80 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	81 <when value="1">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	82 <expand macro="FSsites_br1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	83 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	84 <when value="2" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	85 <expand macro="FSsites_br2_and_3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	86 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	87 <when value="3" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	88 <expand macro="FSsites_br2_and_3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	89 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	90 </conditional>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	91
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	92 <!-- advanced parameters -->
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	93 <section name="adv" title="Advanced Options" expanded="False" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	94 <param argument="verbose" type="select" label="Set the level of details in the log file">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	95 <option value="0" selected="true">0 : concise output</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	96 <option value="1">1 : detailed output</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	97 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	98
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	99 <param argument="runmode" type="select" label="Tree analysis mode" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	100 <option value="0" selected="true">0 : user tree</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	101 <option value="1">1 : heuristic tree search starting from a multifurcating tree from the tree structure file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	102 <option value="2">2 : heuristic tree search starting from the tree file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	103 <option value="3">3 : StepwiseAddition</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	104 <option value="4">4 : PerturbationNNI with the starting tree obtained by a parsimony algorithm</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	105 <option value="5">5 : PerturbationNNI with the starting tree read from the tree structure file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	106 <option value="-2">-2 : ML estimation of dS and dN in pairwise comparisons of protein-coding sequences</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	107 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	108
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	109 <param argument="seqtype" type="select" label="Sequences format in the fasta file" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	110 <option value="1" selected="true">1 : codons</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	111 <option value="2">2 : Amino acids (only compatible with FSsites=0) </option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	112 <option value="3">3 : codons-->amino acids (only compatible with FSsites=0)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	113 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	114
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	115 <param argument="CodonFreq" type="select" label="Equilibrium codon frequencies in codon substitution model">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	116 <option value="0">0 : 1/61 each:</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	117 <option value="1" selected="true">1 : FIX4</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	118 <option value="2">2 : codon table</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	119 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	120
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	121 <param argument="clock" type="select" label="Specifies models concerning rate constancy or variation among lineages" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	122 <option value="0" selected="true">0 : no clock ; An unrooted tree should be used under this model</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	123 <option value="1">1 : clock</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	124 <option value="2">2 : local clock (needed : branch labels in the tree)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	125 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	126
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	127 <param argument="aaDist" type="select" label="Amino acid distances" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	128 <option value="0" selected="true">0 : equal (warning : the only one compatible with NSsites and seqtype=codons</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	129 <option value="+">+ : geometric</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	130 <option value="-">- : linear</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	131 <option value="1">1 : G1974</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	132 <option value="2">2 : Miyata</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	133 <option value="3">3 : c</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	134 <option value="4">4 : p</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	135 <option value="5">5 : v</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	136 <option value="6">6 : a</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	137 <option value="7">7 : AAClasses</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	138 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	139
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	140 <param argument="aaRateFile" type="select" label="Amino acide substitution rate matrix" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	141 <option value="wag.dat" selected="true">wag.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	142 <option value="dayhoff.dat">dayhoff.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	143 <option value="jones.dat">jones.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	144 <option value="mtmam.dat">mtmam.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	145 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	146
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	147 <param argument="icode" type="select" label="Icode : specifies the genetic code" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	148 <option value="0" selected="true">0 : universal code</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	149 <option value="1">1 : mammalian mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	150 <option value="3">3 : mold mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	151 <option value="4">4 : invertebrate mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	152 <option value="5">5 : ciliate nuclear code mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	153 <option value="6">6 : echinoderm mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	154 <option value="7">7 : euplotid mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	155 <option value="8">8 : alternative yeast nuclear</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	156 <option value="9">9 : scidian mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	157 <option value="10">10 : blepharisma nuclear</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	158 <option value="11">11 : Yang's regularized code</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	159 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	160
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	161 <param argument="Mgene" type="select" value="0" label="Multiple genes"
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	162 help="Used in combination with option G in the sequence data file, for combined analysis of data from multiple genes or multiple site partitions" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	163 <option value="0">0 : complete homogeneity among genes </option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	164 <option value="1">1 : equivalent to a separate analysis</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	165 <option value="2">2 : different frequency parameters for different genes but the same rate ratio parameters</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	166 <option value="3">3 : different rate ratio parameters and the same frequency parameters</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	167 <option value="4">4 : both different rate ratio parameters and different frequency parameters for different genes </option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	168 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	169
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	170 <param argument="fix_kappa" type="select" label="Specifies wether kappa in K80, F84, or HKY85 is fixed or estimated">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	171 <option value="0" selected="true">0 : estimated</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	172 <option value="1">1 : fixed (the next parameter below)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	173 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	174
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	175 <param argument="kappa" type="float" value="2" label="Initial or fixed value of kappa" help="kappa refers to the transition/tranversion rate ratio"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	176
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	177 <param argument="fix_omega" type="select" label="Fixed or estimated omega" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	178 <option value="0" selected="true">0 : estimated</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	179 <option value="1">1 : fixed</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	180 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	181
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	182 <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"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	183
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	184 <param argument="fix_alpha" type="select" label="Estimated or fixed gamma shape parameter" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	185 <option value="0">0 : estimate gamma shape parameter. Not recommended</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	186 <option value="1" selected="true">1 : fix it at alpha (the next parameter below)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	187 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	188
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	189 <param argument="alpha" type="float" value="0" label="Initial or fixed value of alpha (gamma shape parameter)"
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	190 help="0: constant rate. fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	191
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	192 <param argument="Malpha" type="select" label="Different alphas for genes" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	193 <option value="0">0 : one gamma distribution will be applied across all sites (one alpha)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	194 <option value="1">1 : different gamma distribution is used for each gene or codon position (different alphas for genes)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	195 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	196
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	197 <param argument="ncatG" type="integer" value="3" label="# of categories in dG of NSsites models" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	198
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	199 <param argument="fix_rho" type="select" label="Independence or correlation of rates at adjacent sites" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	200 <option value="0">0 : estimate rho</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	201 <option value="1" selected="true">1 : fix it at rho (the next parameter below)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	202 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	203
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	204 <param argument="rho" type="float" value="0" label="Initial or fixed rho" help="fix_rho=1 and rho=0 : independent rates" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	205
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	206 <param argument="getSE" type="select" label="Estimates of the standard errors of estimated parameters." >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	207 <option value="0" selected="true">0 : don't want them</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	208 <option value="1">1 : want S.E.s of estimates</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	209 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	210
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	211 <param argument="RateAncestor" type="select" label="RateAncestor ; set 1 to force the program to do two additional analyses" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	212 <option value="0" selected="true">0 : usually use 0</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	213 <option value="1">1 : model of variable rates across site + empirical Bayesian reconstruction of ancestral sequences</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	214 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	215
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	216 <param argument="Small_Diff" type="float" value=".5e-6" label="Value used in the difference approximation of derivatives"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	217
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	218 <param argument="cleandata" type="select" label="Remove sites with ambiguity data" help="Warning : choosing 'yes' may remove a lot (possibly all) of data.">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	219 <option value="0" selected="true">0 : no (don't remove ambiguous data)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	220 <option value="1">1 : yes (remove ambiguous data)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	221 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	222
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	223 <param argument="fix_blength" type="select" label="branch length dealing" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	224 <option value="0" selected="true">0 : ignore branch lengths</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	225 <option value="-1">-1 : start from random starting points</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	226 <option value="1">1 : initial values as written in the tree file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	227 <option value="2">2 : fixed at values in the tree file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	228 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	229
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	230 <param argument="method" type="select" label="Controls the iteration algorithm for estimating branch lengths" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	231 <option value="0" selected="true">0 : simultaneous (old paml algorithm)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	232 <option value="1">1 : one branch at a time (newly implemented in paml ; does not work with clock=1,2,3)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	233 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	234 </section>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	235 </inputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	236
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	237 <outputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	238 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	239 <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	240 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	241 </data>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	242 <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	243 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	244 </data>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	245 <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	246 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	247 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	248 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	249 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	250 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	251 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	252 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	253 <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	254 <filter>adv['verbose']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	255 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	256 </outputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	257
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	258 <tests>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	259 <test expect_num_outputs="9">
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	260 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	261 <param name="brmodel" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	262 <param name="NSsites" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	263 </conditional>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	264 <param name="adv\|fix_omega" value="0" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	265 <param name="adv\|omega" value="0.2" />
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	266 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	267 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	268 <param name="tree" value="RAxML_bestTree" ftype="nhx" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	269 <output name="twongdn" value="1_2ngdn" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	270 <output name="twongds" value="1_2ngds" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	271 <output name="twongt" value="1_2ngt" />
3 b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	272 <output name="run">
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	273 <assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	274 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	275 <has_text text="Time used:" />
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	276 </assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	277 </output>
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	278 <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	279 </test>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	280 <test expect_num_outputs="9">
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	281 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	282 <param name="brmodel" value="2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	283 <param name="NSsites" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	284 </conditional>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	285 <param name="adv\|fix_omega" value="0" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	286 <param name="adv\|omega" value="0.2" />
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	287 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	288 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	289 <param name="tree" value="tree_model2" ftype="nhx" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	290 <output name="twongdn" value="2_2ngdn" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	291 <output name="twongds" value="2_2ngds" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	292 <output name="twongt" value="2_2ngt" />
3 b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	293 <output name="run">
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	294 <assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	295 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	296 <has_text text="Time used:" />
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	297 </assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	298 </output>
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	299 <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	300 </test>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	301 <test expect_num_outputs="9">
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	302 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	303 <param name="brmodel" value="3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	304 <param name="NSsites" value="2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	305 </conditional>
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	306 <param name="adv\|fix_omega" value="0" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	307 <param name="adv\|omega" value="0.2" />
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	308 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	309 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4 f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	310 <param name="tree" value="tree_model3" ftype="nhx" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	311 <output name="twongdn" value="3_2ngdn" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	312 <output name="twongds" value="3_2ngds" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628" iuc parents: 3 diff changeset	313 <output name="twongt" value="3_2ngt" />
3 b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	314 <output name="run">
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	315 <assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	316 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	317 <has_text text="Time used:" />
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	318 </assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b" iuc parents: 2 diff changeset	319 </output>
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	320 <output name="ctl" value="3_codeml.ctl" lines_diff="4" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	321 </test>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	322 </tests>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	323
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	324 <help><![CDATA[
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	325 .. class:: infomark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	326
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	327 Galaxy integration Victor Mataigne and ABIMS TEAM.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	328
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	329 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	330
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	331 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	332
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	333 CompCodeML (from paml package)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	334
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	335 A few help is detailed below ; full and detailed codeml readme can be found on the paml website_.
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	336
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	337 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	338
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	339 .. class:: warningmark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	340
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	341 Due to their high number, some parameters incompatibility can remain.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	342
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	343 This Galaxy implementation :
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	344
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	345 - handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	346 - 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).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	347
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	348 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.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	349
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	350 .. class:: infomark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	351
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	352 Known incompatibilities:
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	353
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	354 - 'seqtype' = 3 : only compatible with 'FSsites' = 0.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	355 - 'clock' = 2 : needs branch labels in the tree.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	356 - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	357 - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	358 - 'method' = 1 : does not work with 'clock' different than 0.
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	359
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	360 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	361
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	362 Description
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	363
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	364 .. class:: infomark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	365
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	366 codeML finds positive selection within branches or codons within a tree and a set of sequences.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	367
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	368 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	369
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	370 Input files
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	371
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	372 - a treefile in Newick format (with or without branch lengths).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	373 - a fasta file with sequences from the species of the tree file (one header/sequence per species) and run codeml (from the paml suite).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	374
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	375 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	376
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	377 Parameters
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	378
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	379 Several models are available.
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	380
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	381 - branch models ("model" parameter).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	382 - sites models ("NSsites" parameter, model is left at 0).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	383 - branch-sites models (when model = 2 NSsites=2,3).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	384 - Clade models (when model=3 NSsites=2,3).
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	385
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	386 Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	387
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	388 .. class:: infomark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	389
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	390 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).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	391
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	392 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).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	393
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	394 Other examples of model
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	395
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	396 How to run the branch-site models (A & B in Yang & Nielsen 2002 MBE) ?
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	397 The options are :
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	398
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	399 - Model A: (model=2, NSsites=2).
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	400 - Model B: (model=2, NSsites=3).
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	401
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	402 How to run the M0 (one-ratio) model :
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	403
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	404 model = 0, NSsites= = 0.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	405
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	406 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	407
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	408 Advanced Parameters
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	409
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	410 .. class:: infomark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	411
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	412 See paml complete manual and FAQ on the paml website_.
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	413
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	414 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	415
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	416 Details of some parameters :
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	417
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	418 - 'kappa' denotes the transition/transversion rate ratio.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	419 - '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.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	420
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	421 -> If fix_kappa = 1 (fixed), the value of kappa is the given value
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	422
ba71e26d5bdc 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 = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	424
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	425 - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	426 - 'fix_alpha' works in a similar way that fix_kappa.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	427
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	428 -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	429
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	430 -> 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.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	431
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	432 - 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).
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	433
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	434 -> 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 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	435
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	436 -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	437
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	438 -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	439
ba71e26d5bdc 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 independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	441
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	442 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	443
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	444 Output files
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	445
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	446 - codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	447 - run_codeml : main result file name.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	448 - The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values;
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	449 - lnf, rst and rst1: Supplemental results.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	450 - rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood).
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	451
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	452 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	453
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	454 How to edit manually the tree file : Branch or node labels
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	455
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	456 Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	457
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	458 - 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.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	459 - 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.
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	460 - 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 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	461
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	462 In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	463 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.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	464
1 ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	465 The following trees are equivalent:
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	466 - ((rabbit, rat) $1, human), goat_cow, marsupial);
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0 iuc parents: 0 diff changeset	467 - (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
0 961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	468
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	469 $ is the symbol for clade labels.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	470
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	471 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.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	472
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	473 In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	474 $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.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	475 Equivalent tree with only '#' :
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	476 ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	477 ]]></help>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	478
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	479 <citations>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	480 <citation type="doi">10.1093/molbev/msm088</citation>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	481 </citations>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8 iuc parents: diff changeset	482 </tool>

Mercurial > repos > iuc > codeml

annotate codeml.xml @ 5:dba114391c98 draft default tip