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