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1 <tool id="phyml" name="PhyML" version="0.1.0">
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2 <description> Phylogeny software based on the maximum-likelihood principle </description>
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3 <requirements>
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4 <package name="phyml" version="3.1"/>
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5 </requirements>
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6 <command><![CDATA[
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7 ln -sf $input input_phy;
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8
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9 phyml -i input_phy
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10 $format
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11
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12 -n $nb_data_set
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13 -d $type.type_of_seq
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14
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15 #if ($type.type_of_seq == "nt"):
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16 -t $type.tstv
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17 #end if
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18
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19 -m $type.model
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20
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21 #if (str($bs.bootstrap) in ['0','-1','-2','-4']):
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22 -b $bs.bootstrap
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23 #elif (str($bs.bootstrap) == '1'):
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24 -b $bs.bootstrap.replicate_num
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25 #end if
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26
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27 -f $character_freq
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28 -v $prop_invar
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29 -c $nb_subst_cat
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30 -a $gamma
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31 -s $search_move
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32 -o $optimisation_parameter
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33
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34 > ${stdout_output};
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35 ]]>
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36 </command>
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37 <inputs>
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38 <param name="input" format="txt" type="data" label="Source file" help="Select the input file"/>
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39 <param name="format" type="select" label="Choose between interleaved format or sequential format" display="radio">
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40 <option value="">Interleaved</option>
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41 <option value="--sequential">Sequential</option>
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42 </param>
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43 <param name="nb_data_set" type="integer" value="1" label="Number of data sets"/>
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44
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45 <conditional name="type">
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46 <param name="type_of_seq" type="select" label="Data type" help="Select between nucleic acids or amino acids" display="radio">
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47 <option value="nt">Nucleic acids</option>
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48 <option value="aa">Amino acids</option>
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49 </param>
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50 <when value="nt">
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51 <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Can be a fixed positive value or type 'e' to get the maximum likelihood estimate"/>
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52 <param name="model" type="select" label="Nucleotide-based models" display="radio">
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53 <option value="HKY85">HKY85</option>
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54 <option value="JC69">JC69</option>
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55 <option value="K80">K80</option>
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56 <option value="F81">F81</option>
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57 <option value="F84">F84</option>
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58 <option value="TN93">TN93</option>
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59 <option value="GTR">GTR</option>
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60 </param>
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61 </when>
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62
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63 <when value="aa">
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64 <param name="model" type="select" label="Amino-acid based models" display="radio">
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65 <option value="LG">LG</option>
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66 <option value="WAG">WAG</option>
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67 <option value="JTT">JTT</option>
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68 <option value="MtREV">MtREV</option>
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69 <option value="Dayhoff">Dayhoff</option>
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70 <option value="DCMut">DCMut</option>
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71 <option value="RtREV">RtREV</option>
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72 <option value="CpREV">CpREV</option>
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73 <option value="VT">VT</option>
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74 <option value="Blosum62">Blosum62</option>
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75 <option value="MtMam">MtMam</option>
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76 <option value="MtArt">MtArt</option>
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77 <option value="HIVw">HIVw</option>
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78 <option value="HIVb">HIVb</option>
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79 </param>
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80 </when>
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81 </conditional>
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82
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83 <conditional name="bs">
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84 <param name="bootstrap" type="select" min="1" value="100" label="Branch supports" display="radio">
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85 <option value="0">No bootstrap</option>
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86 <option value="1">Number of bootstrap</option>
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87 <option value="-1">Likelihood ratio test using aLRT statistics</option>
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88 <option value="-2">Likelihood ratio test using Chi2</option>
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89 <option value="-4" selected='true'>SH-like</option>
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90 </param>
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91 <when value="1">
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92 <param name="replicate_num" type="integer" min="1" value="100" label="Number of bootstrap replicates"/>
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93 </when>
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94 </conditional>
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95
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96 <param name="character_freq" type="select" label="Character frequencies" display="radio">
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97 <option value="e">Empirical</option>
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98 <option value="m">ML/Model</option>
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99 </param>
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100 <param name="prop_invar" type="text" value="e" label="Proportion of invariable sites" help="Can be a fixed value in the [0,1] range or type 'e' to get the maximum likelihood estimate"/>
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101 <param name="nb_subst_cat" type="integer" min="1" value="4" label="Number of relative substitution rate categories" help="Must be a positive integer"/>
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102 <param name="gamma" type="text" value="e" label="Value of the gamma shape parameter" help="Can be a fixed positive value or 'e' to get the maximum likelihood estimate"/>
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103 <param name="search_move" type="select" label="Tree topology search operation option" display="radio">
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104 <option value="NNI">NNI</option>
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105 <option value="SPR">SPR</option>
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106 <option value="BEST">Best of NNI and SPR search</option>
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107 </param>
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108 <param name="optimisation_parameter" type="select" label="Optimise topology" display="radio">
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109 <option value="tlr">Tree topology, branch length and substitution rate parameters</option>
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110 <option value="tl">Tree topology and branch lengths</option>
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111 <option value="lr">Branch lengths and substitution rate parameters</option>
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112 <option value="l">Branch lengths</option>
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113 <option value="r">Substitution rate parameters</option>
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114 <option value="n">No parameter is optimized</option>
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115 </param>
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116 </inputs>
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117
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118 <outputs>
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119 <data name="output_tree" format="txt" label="Output_tree" from_work_dir="*_phyml_tree.txt"/>
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120 <data name="output_stats" format="txt" label="Output_stats" from_work_dir="*_phyml_stats.txt"/>
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121 <data name="stdout_output" label="Output_stdout" format="txt"/>
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122 </outputs>
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123
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124 </tool>
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125
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126
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127
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