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1 <tool id="gd_phylogenetic_tree" name="Phylogenetic" version="1.0.0">
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2 <description>tree</description>
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3
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4 <command interpreter="python">
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5 phylogenetic_tree.py "$input"
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6 #if $individuals.choice == '0'
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7 "all_individuals"
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8 #else if $individuals.choice == '1'
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9 "$p1_input"
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10 #end if
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11 "$output" "$output.extra_files_path" "$minimum_coverage" "$minimum_quality"
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12 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
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13 "none"
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14 #else
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15 "$input.metadata.dbkey"
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16 #end if
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17 "$data_source"
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18 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
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19 #if $draw_tree_options == ''
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20 ""
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21 #else
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22 "-$draw_tree_options"
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23 #end if
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24 #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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25 #set $arg = '%s:%s' % ($individual_col, $individual_name)
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26 "$arg"
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27 #end for
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28 </command>
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29
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30 <inputs>
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31 <param name="input" type="data" format="wsf" label="SNP table" />
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32
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33 <conditional name="individuals">
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34 <param name="choice" type="select" label="Individuals">
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35 <option value="0" selected="true">All</option>
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36 <option value="1">Individuals in a population</option>
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37 </param>
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38 <when value="0" />
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39 <when value="1">
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40 <param name="p1_input" type="data" format="ind" label="Population individuals" />
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41 </when>
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42 </conditional>
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43
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44 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum coverage" help="Note: Minimum coverage and Minimum quality cannot both be 0" />
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45
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46 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum quality" help="Note: Minimum coverage and Minimum quality cannot both be 0" />
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47
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48 <param name="include_reference" type="select" format="integer" label="Include reference sequence">
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49 <option value="1" selected="true">Yes</option>
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50 <option value="0">No</option>
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51 </param>
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52
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53 <param name="data_source" type="select" format="integer" label="Data source">
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54 <option value="0" selected="true">sequence coverage</option>
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55 <option value="1">estimated genotype</option>
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56 </param>
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57
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58 <param name="branch_style" type="select" display="radio">
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59 <label>Branch type</label>
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60 <option value="" selected="true">square</option>
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61 <option value="d">diagonal</option>
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62 </param>
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63
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64 <param name="scale_style" type="select" display="radio">
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65 <label>Draw branches to scale</label>
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66 <option value="" selected="true">yes</option>
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67 <option value="s">no</option>
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68 </param>
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69
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70 <param name="length_style" type="select" display="radio">
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71 <label>Show branch lengths</label>
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72 <option value="" selected="true">yes</option>
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73 <option value="b">no</option>
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74 </param>
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75
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76 <param name="layout_style" type="select" display="radio">
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77 <label>Tree layout</label>
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78 <option value="" selected="true">horizontal</option>
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79 <option value="v">vertical</option>
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80 </param>
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81 </inputs>
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82
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83 <outputs>
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84 <data name="output" format="html" />
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85 </outputs>
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86
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87 <tests>
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88 <test>
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89 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
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90 <param name="choice" value="0" />
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91 <param name="minimum_coverage" value="3" />
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92 <param name="minimum_quality" value="30" />
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93 <param name="data_source" value="0" />
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94 <param name="branch_style" value="" />
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95 <param name="scale_style" value="" />
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96 <param name="length_style" value="" />
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97 <param name="layout_style" value="" />
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98 <output name="output" file="genome_diversity/test_out/phylogenetic_tree/phylogenetic_tree.html" ftype="html" compare="diff" lines_diff="2">
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99 <extra_files type="file" name='distance_matrix.phylip' value="genome_diversity/test_out/phylogenetic_tree/distance_matrix.phylip" />
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100 <extra_files type="file" name='informative_snps.txt' value="genome_diversity/test_out/phylogenetic_tree/informative_snps.txt" />
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101 <extra_files type="file" name='mega_distance_matrix.txt' value="genome_diversity/test_out/phylogenetic_tree/mega_distance_matrix.txt" />
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102 <extra_files type="file" name='phylogenetic_tree.newick' value="genome_diversity/test_out/phylogenetic_tree/phylogenetic_tree.newick" />
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103 <extra_files type="file" name='tree.pdf' value="genome_diversity/test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/>
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104 </output>
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105 </test>
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106 </tests>
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107
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108 <help>
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109 **What it does**
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110
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111 This tool uses a SNP table to determine a kind of "genetic distance" between
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112 each pair of individuals. Optionally, that information can be used to
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113 produce a tree-shaped figure that depicts how the individuals are related,
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114 either as a text file in a common format, called NEWICK, or as a picture.
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115 The user specifies the following inputs to the tool.
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116
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117 SNP table
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118
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119 Individuals
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120 By default, all individuals are included in the analysis; an option
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121 is to analyze only a subset of individuals that has been specified
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122 using the tool to "Select individuals from a SNP table".
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123
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124 Minimum coverage
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125 For each pair of individuals, the tool looks for informative SNPs, i.e.,
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126 where the sequence data for both individuals is adequate according to
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127 some criterion. Specifying, say, 7 for this option instructs the tool
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128 to consider only SNPs with coverage at least 7 in both individuals
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129 when estimating their "genetic distance".
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130
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131 Minimum quality
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132 Specifying, say, 37 for this option instructs the tool to consider
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133 only SNPs with SAMtools quality value at least 37 in both individuals
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134 when estimating their "genetic distance".
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135
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136 Minimum number of informative SNPs
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137 This option instructs the tool to terminate execution if at least one
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138 pair of individuals does not have a required number of informative SNPs.
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139
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140 Include reference sequence
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141 For SNP tables with a reference sequence, the user can ask that the
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142 reference be indicated in the tree, to help with rooting it. If the
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143 SNP table has no reference sequence, this option has no effect.
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144
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145 Data source
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146 The genetic distance between two individuals at a given SNP can
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147 be estimated two ways. One method is to use the absolute value of
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148 difference in the frequency of the first allele (equivalently: the
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149 second allele). For instance, if the first individual has 5 reads of
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150 each allele and the second individual has respectively 3 and 6 reads,
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151 then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that
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152 SNP. The other approach is to use the SAMtools genotypes to estimate
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153 the difference in the number of occurrences of the first allele.
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154 For instance, if the two genotypes are 2 and 1, i.e., the individuals
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155 are estimated to have respectively 2 and 1 occurrences of the first
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156 allele at this location, then the distance is 1 (the absolute value
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157 of the difference of the two numbers).
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158
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159 Output format
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160 There are three options, as described above.
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161
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162 **Acknowledgments**
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163
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164 To convert the distance matrix to a NEWICK-formatted tree, we use the QuickTree program, downloaded from: http://www.sanger.ac.uk/resources/software/quicktree/
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165
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166 To draw the tree, we use the program draw_tree, downloaded from: http://compgen.bscb.cornell.edu/phast/
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167 </help>
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168 </tool>
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