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comparison inbreeding_and_kinship.xml @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
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1 <tool id="gd_inbreeding_and_kinship" name="Inbreeding and kinship" version="1.0.0">
2 <description>: Analyze the pedigree without genomic data</description>
3
4 <command interpreter="python">
5 inbreeding_and_kinship.py '$ped_input' '$ind_input' '$computed_value' '$output'
6 #if $kinship_dataset.choice == '0'
7 '/dev/null'
8 #else if $kinship_dataset.choice == '1'
9 '$kinship_input'
10 #end if
11 </command>
12
13 <inputs>
14 <param name="ped_input" type="data" format="txt" label="Pedigree dataset" />
15 <param name="ind_input" type="data" format="txt" label="Individuals dataset" />
16 <conditional name="kinship_dataset">
17 <param name="choice" type="select" format="integer" label="Kinship dataset">
18 <option value="0" selected="true">no kinship dataset</option>
19 <option value="1">select kinship dataset</option>
20 </param>
21 <when value="0" />
22 <when value="1">
23 <param name="kinship_input" type="data" format="txt" label="Kinship dataset" />
24 </when>
25 </conditional>
26 <param name="computed_value" type="select" format="integer" label="Computed value">
27 <option value="0" selected="true">inbreeding coeffiecients</option>
28 <option value="1">kinships</option>
29 <option value="2">mean kinships</option>
30 </param>
31 </inputs>
32
33 <outputs>
34 <data name="output" format="txt" />
35 </outputs>
36
37 <requirements>
38 <requirement type="package" version="0.1">gd_c_tools</requirement>
39 </requirements>
40
41 <!--
42 <tests>
43 </tests>
44 -->
45
46 <help>
47
48 **Dataset formats**
49
50 The input datasets are in text_ format.
51 The output dataset is in text_ format.
52
53 .. _text: ./static/formatHelp.html#text
54
55 -----
56
57 **What it does**
58
59 The user specifies a pedigree. This is done with a Galaxy table with one
60 row per individual, containing (1) the individual's name, (2) the name of
61 one of the individual's parents, which must have occurred at the start
62 of a previous line, and (3) the name of the individual's other parent,
63 which occurred at the start of a previous line. For a pedigree founder,
64 each parent name is replaced by &quot;-&quot;.
65
66 The user also provides a file that specifies a set of names of individuals
67 (specifically the first word on each line (one line per individual);
68 any subsequent information on a line is ignored.
69
70 The user can optionally provide a file giving kinship information for
71 each pair of distinct individuals from the founder set.
72
73 Finally the user picks from among the options:
74
75 1. inbreeding coefficients for each specified individual
76 2. the kinship for each pair of distinct specified individual
77 3. the mean kinship for each specified individual, i.e., the average kinship value for that individual and every specified individual
78
79 The command reports the requested values.
80
81 -----
82
83 **Example**
84
85 - input::
86
87 A - -
88 B - -
89 C - -
90 D - -
91 E - -
92 F A B
93 G A B
94 Thelma A F
95 Louise F G
96
97 Rows can have more than three columns (such as the individual's sex),
98 but only the first three columns affect this command.
99
100 Suppose on the other hand that we select an alternative
101 &quot;founder&quot; set, {A, F, G}. (We require a founder sets to have a
102 member on any ancestral path from Thelma or Louise.) The above pedigree
103 file is then replaced by::
104
105 A - -
106 F - -
107 G - -
108 Thelma A F
109 Louise F G
110
111 The user then also provides a file giving kinship information for each
112 pairs of distinct individuals from the founder set; for the current
113 example, the kinship file is as follows::
114
115 A F 0.25
116 A G 0.25
117 F G 0.25
118
119 since parent-child pairs and siblings both have kinship 0.25. The
120 advantage is that this capability can be used in cases where the kinships
121 of the founders are not initially known, but instead are computationally
122 predicted, e.g., with the Galaxy &quot;Discover&quot; tool.
123 </help>
124 </tool>
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