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