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annotate codeml.xml @ 4:f9cb3a4339c2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
author iuc
date Sat, 27 Nov 2021 09:55:34 +0000
parents b2b8e75a962d
children dba114391c98
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f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
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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
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2 <description>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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3 Detects positive selection (paml package)
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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4 </description>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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5
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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6 <macros>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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7 <import>macros.xml</import>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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8 </macros>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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9
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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10 <requirements>
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f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
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11 <requirement type="package" version="@TOOL_VERSION@">paml</requirement>
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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12 </requirements>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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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
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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16 <command><![CDATA[
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66228e9c29d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 29dba85647adf75fd7276d5da0f3cc1b8eda23ea"
iuc
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17 cp '$codeml_ctl' '$ctl' &&
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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18 codeml '$codeml_ctl'
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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19 ]]></command>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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21 <configfiles>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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22 <configfile name="codeml_ctl"><![CDATA[
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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23 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
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24 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
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25 treefile = $tree * tree structure file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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26 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
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27 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
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28 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
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29 * 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
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30 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
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31 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
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32 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
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33 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
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34 * 7:AAClasses
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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35 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
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36 * 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
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37 model = $compat_model.brmodel
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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38 * models for codons:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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39 * 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
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40 * models for AAs or codon-translated AAs:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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41 * 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
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42 * 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
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43 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
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44 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:beta&gamma;
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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45 * 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
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46 * 13:3normal>0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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47 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
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48 Mgene = $adv.Mgene * 0:rates, 1:separate;
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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49 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
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50 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
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51 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
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52 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
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53 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
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54 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
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55 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
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56 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
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57 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
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58 rho = $adv.rho * initial or fixed rho, 0:no correlation
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f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
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59 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
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60 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
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61 Small_Diff = $adv.Small_Diff
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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62 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
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63 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
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64 method = $adv.method * 0: simultaneous; 1: one branch at a time
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65 ]]></configfile>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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66 </configfiles>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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67
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68 <inputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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69 <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
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70 <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
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71
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72 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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73 <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
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74 <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
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75 <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
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76 <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
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77 <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
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78 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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79
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
80 <when value="0" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
81 <expand macro="FSsites_br0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
82 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
83 <when value="1">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
84 <expand macro="FSsites_br1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
85 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
86 <when value="2" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
87 <expand macro="FSsites_br2_and_3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
88 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
89 <when value="3" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
90 <expand macro="FSsites_br2_and_3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
91 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
92 </conditional>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
93
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
94 <!-- advanced parameters -->
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
95 <section name="adv" title="Advanced Options" expanded="False" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
96 <param argument="verbose" type="select" label="Set the level of details in the log file">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
97 <option value="0" selected="true">0 : concise output</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
98 <option value="1">1 : detailed output</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
99 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
100
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
101 <param argument="runmode" type="select" label="Tree analysis mode" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
102 <option value="0" selected="true">0 : user tree</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
103 <option value="1">1 : heuristic tree search starting from a multifurcating tree from the tree structure file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
104 <option value="2">2 : heuristic tree search starting from the tree file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
105 <option value="3">3 : StepwiseAddition</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
106 <option value="4">4 : PerturbationNNI with the starting tree obtained by a parsimony algorithm</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
107 <option value="5">5 : PerturbationNNI with the starting tree read from the tree structure file</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
108 <option value="-2">-2 : ML estimation of dS and dN in pairwise comparisons of protein-coding sequences</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
109 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
110
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
111 <param argument="seqtype" type="select" label="Sequences format in the fasta file" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
112 <option value="1" selected="true">1 : codons</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
113 <option value="2">2 : Amino acids (only compatible with FSsites=0) </option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
114 <option value="3">3 : codons--&gt;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
115 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
116
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
117 <param argument="CodonFreq" type="select" label="Equilibrium codon frequencies in codon substitution model">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
118 <option value="0">0 : 1/61 each:</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
119 <option value="1" selected="true">1 : FIX4</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
120 <option value="2">2 : codon table</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
121 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
122
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
123 <param argument="clock" type="select" label="Specifies models concerning rate constancy or variation among lineages" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
124 <option value="0" selected="true">0 : no clock ; An unrooted tree should be used under this model</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
125 <option value="1">1 : clock</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
126 <option value="2">2 : local clock (needed : branch labels in the tree)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
127 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
128
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
129 <param argument="aaDist" type="select" label="Amino acid distances" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
130 <option value="0" selected="true">0 : equal (warning : the only one compatible with NSsites and seqtype=codons</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
131 <option value="+">+ : geometric</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
132 <option value="-">- : linear</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
133 <option value="1">1 : G1974</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
134 <option value="2">2 : Miyata</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
135 <option value="3">3 : c</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
136 <option value="4">4 : p</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
137 <option value="5">5 : v</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
138 <option value="6">6 : a</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
139 <option value="7">7 : AAClasses</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
140 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
141
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
142 <param argument="aaRateFile" type="select" label="Amino acide substitution rate matrix" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
143 <option value="wag.dat" selected="true">wag.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
144 <option value="dayhoff.dat">dayhoff.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
145 <option value="jones.dat">jones.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
146 <option value="mtmam.dat">mtmam.dat</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
147 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
148
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
149 <param argument="icode" type="select" label="Icode : specifies the genetic code" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
150 <option value="0" selected="true">0 : universal code</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
151 <option value="1">1 : mammalian mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
152 <option value="3">3 : mold mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
153 <option value="4">4 : invertebrate mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
154 <option value="5">5 : ciliate nuclear code mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
155 <option value="6">6 : echinoderm mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
156 <option value="7">7 : euplotid mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
157 <option value="8">8 : alternative yeast nuclear</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
158 <option value="9">9 : scidian mt</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
159 <option value="10">10 : blepharisma nuclear</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
160 <option value="11">11 : Yang's regularized code</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
161 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
162
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
163 <param argument="Mgene" type="select" value="0" label="Multiple genes"
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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parents:
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164 help="Used in combination with option G in the sequence data file, for combined analysis of data from multiple genes or multiple site partitions" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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165 <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
166 <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
167 <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
168 <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:
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169 <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
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170 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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171
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
172 <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
173 <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:
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174 <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
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diff changeset
175 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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176
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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177 <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
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178
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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179 <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
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180 <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
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181 <option value="1">1 : fixed</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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182 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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183
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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184 <param argument="omega" type="float" value="0.2" label="Initial or fixed omega (according to your choice for fix_omega), for codons or codon-based AAs"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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185
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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186 <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
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187 <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
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188 <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
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189 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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190
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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191 <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
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192 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
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193
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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194 <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
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195 <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:
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196 <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
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diff changeset
197 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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198
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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199 <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
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200
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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201 <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
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202 <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
203 <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
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204 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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diff changeset
205
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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206 <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
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diff changeset
207
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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208 <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
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209 <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
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210 <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
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211 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
212
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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213 <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
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214 <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
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215 <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
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diff changeset
216 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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217
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218 <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
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219
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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220 <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
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221 <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
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222 <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
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diff changeset
223 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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224
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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225 <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
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226 <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
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parents:
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227 <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
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228 <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
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229 <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
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230 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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231
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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232 <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
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233 <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
234 <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
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235 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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236 </section>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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237 </inputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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238
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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diff changeset
239 <outputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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240 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
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diff changeset
241 <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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242 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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243 </data>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
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diff changeset
244 <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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diff changeset
245 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
246 </data>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
247 <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
248 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
249 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
250 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
251 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
252 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
253 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
254 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
255 <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${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
256 <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
257 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
258 </outputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
259
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
260 <tests>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
261 <test expect_num_outputs="9">
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
262 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
263 <param name="brmodel" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
264 <param name="NSsites" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
265 </conditional>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
266 <param name="adv|fix_omega" value="0" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
267 <param name="adv|omega" value="0.2" />
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
268 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
269 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
270 <param name="tree" value="RAxML_bestTree" ftype="nhx" />
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="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
272 <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
273 <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
274 <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
275 <assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
276 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
277 <has_text text="Time used:" />
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
278 </assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
279 </output>
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
280 <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
281 </test>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
282 <test expect_num_outputs="9">
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
283 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
284 <param name="brmodel" value="2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
285 <param name="NSsites" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
286 </conditional>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
287 <param name="adv|fix_omega" value="0" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
288 <param name="adv|omega" value="0.2" />
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
289 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
290 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
291 <param name="tree" value="tree_model2" ftype="nhx" />
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="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
293 <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
294 <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
295 <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
296 <assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
297 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
298 <has_text text="Time used:" />
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
299 </assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
300 </output>
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
301 <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
302 </test>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
303 <test expect_num_outputs="9">
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
304 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
305 <param name="brmodel" value="3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
306 <param name="NSsites" value="2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
307 </conditional>
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
308 <param name="adv|fix_omega" value="0" />
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
309 <param name="adv|omega" value="0.2" />
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
310 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
311 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
4
f9cb3a4339c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
iuc
parents: 3
diff changeset
312 <param name="tree" value="tree_model3" ftype="nhx" />
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="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
314 <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
315 <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
316 <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
317 <assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
318 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
319 <has_text text="Time used:" />
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
320 </assert_contents>
b2b8e75a962d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit d187c613bdb8999bfaf46f2da6e6400e9012728b"
iuc
parents: 2
diff changeset
321 </output>
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
322 <output name="ctl" value="3_codeml.ctl" lines_diff="4" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
323 </test>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
324 </tests>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
325
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
326 <help><![CDATA[
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
327 .. class:: infomark
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
328
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329 **Galaxy integration** Victor Mataigne and ABIMS TEAM.
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330
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331 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
0
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332
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333 ----------
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334
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335 **CompCodeML (from paml package)**
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336
1
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337 A few help is detailed below ; full and detailed codeml readme can be found on the paml website_.
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338
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339 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
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340
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341 .. class:: warningmark
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342
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343 Due to their high number, some parameters incompatibility can remain.
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344
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345 This Galaxy implementation :
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346
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347 - handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models).
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348 - warns the user in a help section when an advanced parameter has known incompatibilities (the tool CAN be run, but the output files will be empty).
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349
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350 We recommand to have a look at the full paml manual before looking at the advanced parameters, in order to spot parameters incompatibilities and to know what each model does. If you choose by mistake incompatible parameters, the output files will be empty, except the log file ("run_codeml" output) which will normally explicit the error.
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351
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352 .. class:: infomark
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353
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354 Known incompatibilities:
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355
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356 - 'seqtype' = 3 : only compatible with 'FSsites' = 0.
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357 - 'clock' = 2 : needs branch labels in the tree.
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358 - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
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359 - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
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360 - 'method' = 1 : does not work with 'clock' different than 0.
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361
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362 ----------
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363
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364 **Description**
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365
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366 .. class:: infomark
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367
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368 codeML finds positive selection within branches or codons within a tree and a set of sequences.
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369
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370 ----------
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371
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372 **Input files**
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373
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374 - a treefile in Newick format (with or without branch lengths).
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375 - a fasta file with sequences from the species of the tree file (one header/sequence per species) and run codeml (from the paml suite).
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376
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377 ----------
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378
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379 **Parameters**
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380
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381 Several models are available.
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382
0
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383 - branch models ("model" parameter).
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384 - sites models ("NSsites" parameter, model is left at 0).
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385 - branch-sites models (when model = 2 NSsites=2,3).
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386 - Clade models (when model=3 NSsites=2,3).
1
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387
0
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388 Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.
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389
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390 .. class:: infomark
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391
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392 Branch models allow the omega ratio to vary among branches in the phylogeny and are useful for detecting positive selection acting on particular lineages. Sites models allow the omega ratio to vary among sites (codons or amino acids).
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393
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394 Two pairs of models appear to be particularly useful, forming two likelihood ratio tests of positive selection. The first compares M1a ('NearlyNeutral', NSsites=1) and M2a ('PositiveSelection', NSsites=2), while the second compares M7 ('beta', NSsites=7) and M8 ('beta&ω', NSsites=8).
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395
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396 **Other examples of model**
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397
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398 How to run the branch-site models (A &amp; B in Yang &amp; Nielsen 2002 MBE) ?
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399 The options are :
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400
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401 - Model A: (model=2, NSsites=2).
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402 - Model B: (model=2, NSsites=3).
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403
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404 How to run the M0 (one-ratio) model :
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405
0
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406 model = 0, NSsites= = 0.
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407
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408 ----------
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409
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410 **Advanced Parameters**
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411
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412 .. class:: infomark
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413
1
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414 See paml complete manual and FAQ on the paml website_.
0
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415
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416 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
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417
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418 **Details of some parameters :**
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419
1
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420 - 'kappa' denotes the transition/transversion rate ratio.
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421 - 'fix_kappa' specifies whether kappa in K80, F84, or HKY85 is given at a fixed value or is to be estimated by iteration from the data.
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422
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423 -> If fix_kappa = 1 (fixed), the value of kappa is the given value
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424
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425 -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
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426
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427 - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
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428 - 'fix_alpha' works in a similar way that fix_kappa.
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429
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430 -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
0
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431
1
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432 -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable.
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433
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434 - fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995).
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435
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436 -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites.
0
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437
1
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438 -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
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439
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440 -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
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441
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442 -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
0
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443
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444 ----------
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445
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446 **Output files**
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447
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448 - codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run).
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449 - run_codeml : main result file name.
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450 - The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values;
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451 - lnf, rst and rst1: Supplemental results.
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452 - rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood).
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453
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454 ----------
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455
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456 **How to edit manually the tree file : Branch or node labels**
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457
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458 Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
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459
1
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460 - For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively.
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461 - Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models.
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462 - All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified.
0
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463
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464 In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
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465 The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0.
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466
1
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467 The following trees are equivalent:
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468 - ((rabbit, rat) $1, human), goat_cow, marsupial);
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469 - (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
0
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470
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471 $ is the symbol for clade labels.
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472
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473 Rules concerning nested clade labels : The symbol # takes precedence over the symbol $, and clade labels close to the tips take precedence over clade labels for ancestral nodes close to the root.
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474
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475 In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
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476 $1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade.
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477 Equivalent tree with only '#' :
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478 ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
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479 ]]></help>
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480
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481 <citations>
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482 <citation type="doi">10.1093/molbev/msm088</citation>
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483 </citations>
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484 </tool>