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annotate codeml.xml @ 1:ba71e26d5bdc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
author iuc
date Wed, 02 May 2018 05:44:08 -0400
parents 961a712f9743
children 66228e9c29d9
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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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1 <tool name="codeML" id="codeml" version="1.0">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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2 <description>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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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
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4 </description>
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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
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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
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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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11 <requirement type="package" version="4.9">paml</requirement>
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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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13
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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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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15
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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16 <command><![CDATA[
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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17 codeml '$codeml_ctl'
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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18 &&
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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19 mv '$codeml_ctl' '$ctl'
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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20 ]]></command>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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21
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22 <configfiles>
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23 <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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24 seqfile = $concat_nuc * sequence data file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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25 outfile = run_codeml * main result file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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26 treefile = $tree * tree structure file name
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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27 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
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28 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
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29 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
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30 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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31 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
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32 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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33 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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34 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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35 * 7:AAClasses
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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36 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
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37 * 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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38 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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39 * models for codons:
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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40 * 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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41 * 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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42 * 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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43 * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
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44 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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45 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:beta&gamma;
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46 * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
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47 * 13:3normal>0
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48 icode = $adv.icode * 0:universal code; 1:mammalian mt; 2-11:see below
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49 Mgene = $adv.Mgene * 0:rates, 1:separate;
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50 fix_kappa = $adv.fix_kappa * 1: kappa fixed, 0: kappa to be estimated
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51 kappa = $adv.kappa * initial or fixed kappa
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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52 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
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53 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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54 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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55 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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56 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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57 ncatG = $adv.ncatG * # of categories in dG of NSsites models
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58 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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59 rho = $adv.rho * initial or fixed rho, 0:no correlation
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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60 getSE = $adv.getSE * 0: don't want them, 1: want S.E.s of estimates
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61 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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62 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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63 cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)?
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64 fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed
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65 method = $adv.method * 0: simultaneous; 1: one branch at a time
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66 ]]></configfile>
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67 </configfiles>
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68
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69 <inputs>
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70 <param name="concat_nuc" type="data" format="fasta" label="Sequences file" help="The fasta file with the sequences to be analyzed" />
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71 <param name="tree" type="data" format="nhx" label="tree file" help="Tree file in Newick format" />
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72
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73 <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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74 <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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75 <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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76 <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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77 <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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78 <option value="3">'3' : clade-model ; implies to manually edit your tree file</option>
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79 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
80
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
81 <when value="0" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
82 <expand macro="FSsites_br0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
83 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
84 <when value="1">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
85 <expand macro="FSsites_br1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
86 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
87 <when value="2" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
88 <expand macro="FSsites_br2_and_3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
89 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
90 <when value="3" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
91 <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
92 </when>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
93 </conditional>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
94
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
95 <!-- advanced parameters -->
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
96 <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
97 <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
98 <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
99 <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
100 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
101
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
102 <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
103 <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
104 <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
105 <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
106 <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
107 <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
108 <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
109 <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
110 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
111
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
112 <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
113 <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
114 <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
115 <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
116 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
117
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
118 <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
119 <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
120 <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
121 <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
122 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
123
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
124 <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
125 <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
126 <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
127 <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
128 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
129
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
130 <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
131 <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
132 <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
133 <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
134 <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
135 <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
136 <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
137 <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
138 <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
139 <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
140 <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
141 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
142
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
143 <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
144 <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
145 <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
146 <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
147 <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
148 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
149
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
150 <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
151 <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
152 <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
153 <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
154 <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
155 <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
156 <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
157 <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
158 <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
159 <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
160 <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
161 <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
162 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
163
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
164 <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:
diff changeset
165 help="Used in combination with option G in the sequence data file, for combined analysis of data from multiple genes or multiple site partitions" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
166 <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
167 <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
168 <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
169 <option value="3">3 : different rate ratio parameters and the same frequency parameters</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
170 <option value="4">4 : both different rate ratio parameters and different frequency parameters for different genes </option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
171 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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172
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
173 <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
174 <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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175 <option value="1">1 : fixed (the next parameter below)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
176 </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
177
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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178 <param argument="kappa" type="float" value="2" label="Initial or fixed value of kappa" help="kappa refers to the transition/tranversion rate ratio"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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179
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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180 <param argument="fix_omega" type="select" label="Fixed or estimated omega" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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181 <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
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182 <option value="1">1 : fixed</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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183 </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
184
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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185 <param argument="omega" type="float" value="0.2" label="Initial or fixed omega (according to your choice for fix_omega), for codons or codon-based AAs"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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186
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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187 <param argument="fix_alpha" type="select" label="Estimated or fixed gamma shape parameter" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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188 <option value="0">0 : estimate gamma shape parameter. Not recommended</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
189 <option value="1" selected="true">1 : fix it at alpha (the next parameter below)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
190 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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191
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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192 <param argument="alpha" type="float" value="0" label="Initial or fixed value of alpha (gamma shape parameter)"
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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193 help="0: constant rate. fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
194
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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195 <param argument="Malpha" type="select" label="Different alphas for genes" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
196 <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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197 <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
198 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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199
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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200 <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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diff changeset
201
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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202 <param argument="fix_rho" type="select" label="Independence or correlation of rates at adjacent sites" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
203 <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
204 <option value="1" selected="true">1 : fix it at rho (the next parameter below)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
205 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
206
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
207 <param argument="rho" type="float" value="0" label="Initial or fixed rho" help="fix_rho=1 and rho=0 : independent rates" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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208
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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209 <param argument="getSE" type="select" label="Estimates of the standard errors of estimated parameters." >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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210 <option value="0" selected="true">0 : don't want them</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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211 <option value="1">1 : want S.E.s of estimates</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
212 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
213
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
214 <param argument="RateAncestor" type="select" label="RateAncestor ; set 1 to force the program to do two additional analyses" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
215 <option value="0" selected="true">0 : usually use 0</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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216 <option value="1">1 : model of variable rates across site + empirical Bayesian reconstruction of ancestral sequences</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
217 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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218
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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219 <param argument="Small_Diff" type="float" value=".5e-6" label="Value used in the difference approximation of derivatives"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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220
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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221 <param argument="cleandata" type="select" label="Remove sites with ambiguity data" help="Warning : choosing 'yes' may remove a lot (possibly all) of data.">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
222 <option value="0" selected="true">0 : no (don't remove ambiguous data)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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223 <option value="1">1 : yes (remove ambiguous data)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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224 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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225
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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226 <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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227 <option value="0" selected="true">0 : ignore branch lengths</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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228 <option value="-1">-1 : start from random starting points</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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229 <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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230 <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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231 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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232
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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233 <param argument="method" type="select" label="Controls the iteration algorithm for estimating branch lengths" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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234 <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
235 <option value="1">1 : one branch at a time (newly implemented in paml ; does not work with clock=1,2,3)</option>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
236 </param>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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237 </section>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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238 </inputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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239
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
240 <outputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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241 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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242 <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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243 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
244 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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245 <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
246 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
247 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
248 <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
249 <filter>adv['seqtype']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
250 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
251 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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252 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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253 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
254 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
255 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
256 <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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257 <filter>adv['verbose']=="1"</filter>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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258 </data>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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259 </outputs>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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260
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
261 <tests>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
262 <test>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
263 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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264 <param name="brmodel" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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265 <param name="NSsites" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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266 </conditional>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
267 <param name="adv.fix_omega" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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268 <param name="adv.omega" value="0.2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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269 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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270 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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271 <param name="tree" ftype="txt" value="RAxML_bestTree" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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272 <output name="2ngdn" value="1_2ngdn" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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273 <output name="2ngds" value="1_2ngds" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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274 <output name="2ngt" value="1_2ngt" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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275 <output name="run" value="1_run_codeml" lines_diff="20"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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276 <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
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277 </test>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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278 <test>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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279 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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280 <param name="brmodel" value="2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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281 <param name="NSsites" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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282 </conditional>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
283 <param name="adv.fix_omega" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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284 <param name="adv.omega" value="0.2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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285 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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286 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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287 <param name="tree" ftype="txt" value="tree_model2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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288 <output name="2ngdn" value="2_2ngdn" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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289 <output name="2ngds" value="2_2ngds" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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290 <output name="2ngt" value="2_2ngt" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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291 <output name="run" value="2_run_codeml" lines_diff="20" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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292 <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
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293 </test>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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294 <test>
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295 <conditional name="compat_model" >
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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296 <param name="brmodel" value="3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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297 <param name="NSsites" value="2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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298 </conditional>
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iuc
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diff changeset
299 <param name="adv.fix_omega" value="0" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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300 <param name="adv.omega" value="0.2" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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301 <param name="RateAncestor" value="1" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
302 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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303 <param name="tree" ftype="txt" value="tree_model3" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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304 <output name="2ngdn" value="3_2ngdn" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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305 <output name="2ngds" value="3_2ngds" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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306 <output name="2ngt" value="3_2ngt" />
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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307 <output name="run" value="3_run_codeml" lines_diff="20"/>
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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308 <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
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309 </test>
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310 </tests>
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311
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iuc
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312 <help><![CDATA[
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313 .. class:: infomark
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diff changeset
314
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
315 **Galaxy integration** Victor Mataigne and ABIMS TEAM.
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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316
1
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
iuc
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diff changeset
317 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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318
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319 ----------
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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320
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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321 **CompCodeML (from paml package)**
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322
1
ba71e26d5bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
iuc
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diff changeset
323 A few help is detailed below ; full and detailed codeml readme can be found on the paml website_.
0
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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324
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325 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
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326
961a712f9743 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
327 .. class:: warningmark
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328
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329 Due to their high number, some parameters incompatibility can remain.
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330
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331 This Galaxy implementation :
1
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332
0
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333 - handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models).
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334 - 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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335
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336 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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337
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338 .. class:: infomark
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339
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340 Known incompatibilities:
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341
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342 - 'seqtype' = 3 : only compatible with 'FSsites' = 0.
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343 - 'clock' = 2 : needs branch labels in the tree.
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344 - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
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345 - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
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346 - 'method' = 1 : does not work with 'clock' different than 0.
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347
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348 ----------
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349
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350 **Description**
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351
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352 .. class:: infomark
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353
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354 codeML finds positive selection within branches or codons within a tree and a set of sequences.
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355
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356 ----------
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357
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358 **Input files**
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359
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360 - a treefile in Newick format (with or without branch lengths).
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361 - 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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362
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363 ----------
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364
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365 **Parameters**
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366
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367 Several models are available.
1
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368
0
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369 - branch models ("model" parameter).
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370 - sites models ("NSsites" parameter, model is left at 0).
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371 - branch-sites models (when model = 2 NSsites=2,3).
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372 - Clade models (when model=3 NSsites=2,3).
1
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373
0
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374 Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.
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375
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376 .. class:: infomark
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377
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378 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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379
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380 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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381
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382 **Other examples of model**
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383
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384 How to run the branch-site models (A &amp; B in Yang &amp; Nielsen 2002 MBE) ?
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385 The options are :
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386
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387 - Model A: (model=2, NSsites=2).
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388 - Model B: (model=2, NSsites=3).
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389
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390 How to run the M0 (one-ratio) model :
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391
0
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392 model = 0, NSsites= = 0.
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393
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394 ----------
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395
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396 **Advanced Parameters**
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397
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398 .. class:: infomark
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399
1
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400 See paml complete manual and FAQ on the paml website_.
0
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401
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402 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
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403
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404 **Details of some parameters :**
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405
1
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406 - 'kappa' denotes the transition/transversion rate ratio.
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407 - '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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408
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409 -> If fix_kappa = 1 (fixed), the value of kappa is the given value
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410
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411 -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
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412
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413 - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
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414 - 'fix_alpha' works in a similar way that fix_kappa.
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415
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416 -> 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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417
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418 -> 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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419
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420 - 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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421
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422 -> 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.
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423
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424 -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
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425
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426 -> 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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427
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428 -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
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429
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430 ----------
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431
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432 **Output files**
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433
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434 - codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run).
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435 - run_codeml : main result file name.
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436 - The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values;
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437 - lnf, rst and rst1: Supplemental results.
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438 - rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood).
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439
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440 ----------
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441
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442 **How to edit manually the tree file : Branch or node labels**
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443
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444 Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
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445
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446 - 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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447 - 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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448 - 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.
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449
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450 In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
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451 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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452
1
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453 The following trees are equivalent:
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454 - ((rabbit, rat) $1, human), goat_cow, marsupial);
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455 - (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
0
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456
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457 $ is the symbol for clade labels.
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458
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459 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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460
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461 In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
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462 $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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463 Equivalent tree with only '#' :
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464 ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
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465 ]]></help>
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466
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467 <citations>
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468 <citation type="doi">10.1093/molbev/msm088</citation>
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469 </citations>
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470 </tool>