annotate phylogenetic_tree.xml @ 39:e56023008e36 default tip

Changed revision of package_fisher_0_1_4 to be2fc454d121 Changed revision of package_matplotlib_1_2 to a03ee94316b5
author miller-lab
date Mon, 06 Jul 2015 10:32:24 -0400
parents a631c2f6d913
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
1 <tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.1.0">
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
2 <description>: Show genetic relationships among individuals</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
4 <command interpreter="python">
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
5 #import json
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
6 #import base64
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
7 #import zlib
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
8 #set $ind_names = $input.dataset.metadata.individual_names
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
9 #set $ind_colms = $input.dataset.metadata.individual_columns
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
12 #set $ind_comp = zlib.compress($ind_json, 9)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
13 #set $ind_arg = base64.b64encode($ind_comp)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
14 phylogenetic_tree.py '$input' '$output' '$output.files_path'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
15 #if $input_type.choice == '0'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
16 'gd_snp'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
17 #if $input_type.data_source.choice == '0'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
18 'sequence_coverage'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
19 '$input_type.data_source.minimum_coverage'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
20 '$input_type.data_source.minimum_quality'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
21 #else if $input_type.data_source.choice == '1'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
22 'estimated_genotype' '0' '0'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
23 #end if
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
24 #else if $input_type.choice == '1'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
25 'gd_genotype' 'estimated_genotype' '0' '0'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
26 #end if
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
27 #if $individuals.choice == '0'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
28 'all_individuals'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
29 #else if $individuals.choice == '1'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
30 '$individuals.p1_input'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
31 #end if
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
32 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
33 'none'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
34 #else
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
35 '$input.metadata.dbkey'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
36 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
37 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
38 #if $draw_tree_options == ''
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
39 ''
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
40 #else
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
41 '-$draw_tree_options'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
42 #end if
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
43 '$ind_arg'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
44 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
45
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
46 <inputs>
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
47 <conditional name="input_type">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
48 <param name="choice" type="select" format="integer" label="Input format">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
49 <option value="0" selected="true">gd_snp</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
50 <option value="1">gd_genotype</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
51 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
52 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
53 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
54
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
55 <conditional name="data_source">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
56 <param name="choice" type="select" format="integer" label="Distance metric">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
57 <option value="0">sequence coverage</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
58 <option value="1" selected="true">estimated genotype</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
59 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
60 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
61 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
62 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
63 help="Note: minimum coverage and minimum quality cannot both be 0" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
64 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
65 <when value="1"/>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
66 </conditional>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
67 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
68 <when value="1">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
69 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
70 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
71 </conditional>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
72
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
73 <conditional name="individuals">
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
74 <param name="choice" type="select" label="Compute for">
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
75 <option value="0" selected="true">All individuals</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
76 <option value="1">Individuals in a population</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
77 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
78 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
79 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
80 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
81 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
82 </conditional>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
83
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
84 <param name="include_reference" type="select" format="integer" label="Include reference sequence">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
85 <option value="1" selected="true">Yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
86 <option value="0">No</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
87 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
88
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
89 <param name="branch_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
90 <label>Branch type</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
91 <option value="" selected="true">square</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
92 <option value="d">diagonal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
93 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
94
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
95 <param name="scale_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
96 <label>Draw branches to scale</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
97 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
98 <option value="s">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
99 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
100
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
101 <param name="length_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
102 <label>Show branch lengths</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
103 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
104 <option value="b">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
105 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
106
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
107 <param name="layout_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
108 <label>Tree layout</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
109 <option value="" selected="true">horizontal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
110 <option value="v">vertical</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
111 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
112 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
113
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
114 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
115 <data name="output" format="html" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
116 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
117
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
118 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
119 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
120 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
121 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
122 <param name="minimum_coverage" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
123 <param name="minimum_quality" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
124 <param name="data_source" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
125 <param name="branch_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
126 <param name="scale_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
127 <param name="length_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
128 <param name="layout_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
129 <output name="output" file="test_out/phylogenetic_tree/phylogenetic_tree.html" ftype="html" compare="diff" lines_diff="2">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
130 <extra_files type="file" name="distance_matrix.phylip" value="test_out/phylogenetic_tree/distance_matrix.phylip" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
131 <extra_files type="file" name="informative_snps.txt" value="test_out/phylogenetic_tree/informative_snps.txt" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
132 <extra_files type="file" name="mega_distance_matrix.txt" value="test_out/phylogenetic_tree/mega_distance_matrix.txt" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
133 <extra_files type="file" name="phylogenetic_tree.newick" value="test_out/phylogenetic_tree/phylogenetic_tree.newick" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
134 <extra_files type="file" name="tree.pdf" value="test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
135 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
136 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
137 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
138
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
139 <requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
140 <requirement type="package" version="1.3">phast</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
141 <requirement type="package" version="1.1">quicktree</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
142 <requirement type="package" version="0.1">gd_c_tools</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
143 </requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
144
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
145
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
146 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
147
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
148 **Dataset formats**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
149
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
150 The input dataset is in gd_snp_ or gd_genotype_ format.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
151 The output is a composite dataset, containing the tree in both text (Newick_)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
152 and PostScript formats, as well as supplemental text information.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
153 (`Dataset missing?`_)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
154
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
155 .. _gd_snp: ./static/formatHelp.html#gd_snp
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
156 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
157 .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
158 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
159
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
160 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
161
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
162 **What it does**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
163
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
164 This tool uses a gd_snp dataset to determine a kind of "genetic distance"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
165 between each pair of individuals. That information is used to
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
166 produce a tree-shaped figure that depicts how the individuals are related,
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
167 both as a text files and as a diagram.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
168 The text files include a common tree format, Newick, as well as distance
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
169 matrices and counts of informative SNPs for each pairwise comparison.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
170 The informative SNPs can be used as a guide to how reliable the tree is.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
171
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
172 The input parameters are:
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
173
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
174 SNP dataset
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
175 A table of SNPs for various individuals, in gd_snp format.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
176
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
177 Individuals
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
178 By default all individuals are included in the analysis, but this can
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
179 optionally be restricted to a subset that has been defined using the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
180 Specify Individuals tool.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
181
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
182 Minimum SNP coverage
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
183 For each pair of individuals, the tool looks for informative SNPs, i.e.,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
184 where the sequence data for both individuals is adequate. Specifying,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
185 say, 7 for this option instructs the tool to consider only SNPs with
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
186 at least 7 reads in each of the two individuals (regardless of the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
187 alleles) when estimating their genetic distance.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
188
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
189 Minimum SNP quality
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
190 Specifying, say, 37 for this option instructs the tool to consider
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
191 only SNPs with a quality score of at least 37 in both individuals
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
192 when estimating their genetic distance.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
193
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
194 Include reference sequence
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
195 For gd_snp datasets containing columns for a reference sequence, the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
196 user can ask that the reference be indicated in the tree, to help with
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
197 rooting it. If the dataset has no reference columns, this option has
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
198 no effect.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
199
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
200 Distance metric
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
201 The genetic distance between two individuals at a given SNP can
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
202 be estimated two ways. One method is to use the absolute value of the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
203 difference in the frequency of the first allele (or equivalently, the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
204 second allele). For instance, if the first individual has 5 reads of
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
205 each allele and the second individual has respectively 3 and 6 reads,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
206 then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
207 SNP. The other approach is to use the genotype calls to estimate
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
208 the difference in the number of occurrences of the first allele.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
209 For instance, if the two genotypes are 2 and 1, i.e., the individuals
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
210 are estimated to have respectively 2 and 1 occurrences of the first
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
211 allele at this location, then the distance is 1 (the absolute value
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
212 of the difference of the two numbers).
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
213
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
214 Output options
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
215 The final four options apply mostly to the graphical drawing of the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
216 tree, except that the branch lengths are also added to the Newick text
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
217 file.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
218
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
219 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
220
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
221 **Acknowledgments**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
222
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
223 To convert the distance matrix to a Newick-formatted tree, we use the
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
224 QuickTree program from
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
225 http://www.sanger.ac.uk/resources/software/quicktree/ .
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
226
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
227 To make the diagram we use draw_tree, available at
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
228 http://compgen.bscb.cornell.edu/phast/ .
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
229
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
230 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
231 </tool>