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annotate phyml.xml @ 0:a9ee99c3be94 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
author iuc
date Tue, 28 May 2019 13:53:34 -0400
parents
children 2677a6dae0e0
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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1 <tool id="phyml" name="PhyML" version="3.3.20190321">
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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2 <description>Phylogeny software based on the maximum-likelihood</description>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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3 <requirements>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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4 <requirement type="package" version="3.3.20190321">phyml</requirement>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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5 </requirements>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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6 <version_command>
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7 <![CDATA[ phyml --version ]]>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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8 </version_command>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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9 <command detect_errors="default">
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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10 <![CDATA[
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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11 ##PhyML outputs are based on input path and we need to create outputs in working_dir.
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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12 ln -sf '$input' '${input.name}' &&
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
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13 #if $userInputTree:
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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14 ln -sf '${$userInputTree}' '${$userInputTree.name}' &&
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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15 #end if
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16
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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17 phyml --input '${input.name}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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18 '${phylip_format}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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19 --datatype '${seq.type_of_seq}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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20 --multiple '${nb_data_set}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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21
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22 #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']):
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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23 --bootstrap '${support_condition.branchSupport}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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24 #else:
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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25 --bootstrap '${support_condition.branchSupport.replicate}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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26 #end if
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27
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28 #if $seq.type_of_seq == "nt":
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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29 -t '${seq.tstv}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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30 #end if
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31
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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32 --model '${seq.model}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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33 -f '${equi_freq}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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34 --pinv '${prop_invar}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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35
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36 --nclasses '${nbSubstCat}'
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37
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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38 #if (str($nbSubstCat) != "1"):
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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39 --alpha '${gamma}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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40 #end if
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41
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42 --search '${move}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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43 -o '${optimisationTopology}'
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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44
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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45 #if $userInputTree:
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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46 --inputtree '${$userInputTree.name}'
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47 #end if
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48
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49 #if $numStartSeed != "0":
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50 --r_seed '${numStartSeed}'
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51 #end if
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52
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53 --no_memory_check > '${output_stdout}' &&
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54 grep 'failed' '${output_stdout}' >&2;
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55 ]]>
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56 </command>
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57 <inputs>
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58 <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>
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59 <param name="phylip_format" type="select" label="Changes interleaved format">
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60 <option value="">Interleaved</option>
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61 <option value="--sequential">Sequential</option>
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62 </param>
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63 <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" />
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64 <conditional name="seq">
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65 <param name="type_of_seq" type="select" label="Data type">
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66 <option value="nt">Nucleic acids</option>
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67 <option value="aa">Amino acids</option>
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68 </param>
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69 <when value="nt">
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70 <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" />
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71 <param name="model" type="select" label="Substitution model">
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72 <option value="HKY85">HKY85</option>
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73 <option value="JC69">JC69</option>
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74 <option value="K80">K80</option>
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75 <option value="F81">F81</option>
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76 <option value="F84">F84</option>
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77 <option value="TN93">TN93</option>
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78 <option value="GTR">GTR</option>
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79 </param>
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80 </when>
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81 <when value="aa">
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82 <param name="model" type="select" label="Evolution model">
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83 <option value="LG">LG</option>
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84 <option value="WAG">WAG</option>
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85 <option value="JTT">JTT</option>
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86 <option value="MtREV">MtREV</option>
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87 <option value="Dayhoff">Dayhoff</option>
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88 <option value="DCMut">DCMut</option>
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89 <option value="RtREV">RtREV</option>
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90 <option value="CpREV">CpREV</option>
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91 <option value="VT">VT</option>
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92 <option value="Blosum62">Blosum62</option>
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93 <option value="MtMam">MtMam</option>
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94 <option value="MtArt">MtArt</option>
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95 <option value="HIVw">HIVw</option>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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96 <option value="HIVb">HIVb</option>
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97 </param>
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98 </when>
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99 </conditional>
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100 <param name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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101 <param name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.">
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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102 <option value="m">ML/Model</option>
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103 <option value="e">Empirical</option>
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104 </param>
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105 <param name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" />
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106 <param name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/>
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107 <param name="move" type="select" label="Tree topology search">
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108 <option value="NNI">NNI (Nearest Neighbor Interchange)</option>
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109 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>
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110 <option value="BEST">Best of NNI and SPR</option>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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111 </param>
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112 <param name="optimisationTopology" type="select" label="Optimise topology">
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113 <option value="tlr">Tree topology, Branch length, Rate parameter</option>
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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114 <option value="tl">Tree topology, Branch length</option>
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115 <option value="l">Branch length</option>
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116 <option value="r">Rate parameter</option>
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117 <option value="n">No parameter is optimized</option>
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118 </param>
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119 <conditional name="support_condition">
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120 <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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121 <option value="0">No bootstrap</option>
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122 <option value="1">Bootstrap</option>
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123 <option value="-1">likelihood aLRT statistics</option>
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124 <option value="-2">likelihood Chi2-based</option>
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125 <option value="-4" selected='true'>SH-like</option>
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126 <option value="-5">Approximate Bayes branch supports</option>
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127 </param>
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128 <when value="0"/>
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129 <when value="-1"/>
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130 <when value="-2"/>
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131 <when value="-4"/>
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132 <when value="-5"/>
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133 <when value="1">
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134 <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />
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135 </when>
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136 </conditional>
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137 <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/>
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138 <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/>
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139 </inputs>
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140 <outputs>
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141 <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />
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142 <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/>
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143 <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/>
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144 </outputs>
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145 <tests>
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146 <test>
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147 <param name="input" value="phylip" />
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148 <param name="prop_invar" value="0"/>
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149 <param name="type_of_seq" value="nt" />
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150 <param name="numStartSeed" value="1458308600" />
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151 <output name="output_tree" file="phylip_phyml_tree.txt" />
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152 <output name="output_stats" file="phylip_phyml_stats.txt" lines_diff="4"/>
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153 </test>
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154 </tests>
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155 <help>
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156 <![CDATA[
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157 .. class:: infomark
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158
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159 -----
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160
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161 #########
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162 PhyML 3.3
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163 #########
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164
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165 A simple, fast, and accurate algorithm to estimate
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166 large phylogenies by maximum likelihood''
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167
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168 ==========
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169 Overview:
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170 ==========
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171
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172 PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued.
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174 We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task.
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175
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176 It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.
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177
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178 -----
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179
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180
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181 For further informations, please visite the PhyML_ website.
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182
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183 .. _PhyML: http://www.atgc-montpellier.fr/phyml/
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184
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185 Please cite this paper if you use this software in your publications.
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186
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187
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188 ]]>
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189 </help>
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190 <citations>
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191 <citation type="doi">10.1093/sysbio/syq010</citation>
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192 </citations>
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193 </tool>