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annotate coverage_distributions.xml @ 28:184d14e4270d

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Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -0400
parents 8997f2ca8c7a
children a631c2f6d913
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1 <tool id="gd_coverage_distributions" name="Coverage Distributions" version="1.0.0">
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2 <description>: Examine sequence coverage for SNPs</description>
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3
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4 <command interpreter="python">
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5 #import json
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6 #import base64
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7 #import zlib
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8 #set $ind_names = $input.dataset.metadata.individual_names
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9 #set $ind_colms = $input.dataset.metadata.individual_columns
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
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12 #set $ind_comp = zlib.compress($ind_json, 9)
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13 #set $ind_arg = base64.b64encode($ind_comp)
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14 coverage_distributions.py '$input' '0' '$output' '$output.files_path' '$ind_arg'
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15 #if $individuals.choice == '0'
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16 'all_individuals'
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17 #else if $individuals.choice == '1'
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18 #set $arg = 'individuals:%s' % str($individuals.p1_input)
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19 '$arg'
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20 #else if $individuals.choice == '2'
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21 #for $population in $individuals.populations
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22 #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
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23 '$arg'
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24 #end for
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25 #end if
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26 </command>
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27
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28 <inputs>
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29 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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30
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31 <conditional name="individuals">
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32 <param name="choice" type="select" label="Compute for">
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33 <option value="0" selected="true">All individuals</option>
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34 <option value="1">Individuals in a population</option>
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35 <option value="2">Totals of populations</option>
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36 </param>
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37 <when value="0" />
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38 <when value="1">
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39 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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40 </when>
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41 <when value="2">
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42 <repeat name="populations" title="Population" min="1">
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43 <param name="p_input" type="data" format="gd_indivs" label="individuals" />
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44 </repeat>
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45 </when>
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46 </conditional>
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47
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48 <!--
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49 <param name="data_source" type="select" label="Data source">
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50 <option value="0" selected="true">Sequence coverage</option>
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51 <option value="1">Genotype quality</option>
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52 </param>
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53 -->
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54 </inputs>
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55
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56 <outputs>
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57 <data name="output" format="html" />
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58 </outputs>
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59
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60 <tests>
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61 <test>
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62 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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63 <param name="choice" value="0" />
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64 <output name="output" file="test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2">
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65 <extra_files type="file" name="coverage.pdf" value="test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/>
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66 <extra_files type="file" name="coverage.txt" value="test_out/coverage_distributions/coverage.txt" />
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67 </output>
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68 </test>
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69 </tests>
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70
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71 <help>
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72
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73 **Dataset formats**
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74
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75 The input dataset is in gd_snp_ format.
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76 The output is a composite dataset, containing both a text table and a PDF plot.
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77 (`Dataset missing?`_)
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78
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79 .. _gd_snp: ./static/formatHelp.html#gd_snp
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80 .. _Dataset missing?: ./static/formatHelp.html
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81
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82 -----
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83
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84 **What it does**
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85
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86 This tool reports distributions of a SNP reliability indicator, in this case
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87 sequence coverage, for individuals or populations.
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88 The coverage can be computed for all individuals, a subset of individuals,
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89 or totals for populations defined by the Specify Individuals tool.
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90 The results are reported as a text table giving the cumulative distributions,
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91 and as a plot.
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92
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93 -----
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94
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
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95 **Example**
14
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96
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97 - input::
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98
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99 chr1 14929 A G 999 21 30 1 127 7 11 1 28 7 29 0 5 2 5 1 17 10 14 1 81 17 74 1 42 15 22 1 125 29 84 1 88 6 10 1 11 30 23 1 79 19 1 2 71 24 0 2 99 41 10 2 2
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100 chr1 17451 C T 6.88 119 1 2 255 12 0 2 63 35 0 2 59 14 0 2 72 19 1 2 57 101 1 2 255 38 8 1 20 125 0 2 255 13 0 2 62 42 0 2 51 44 0 2 64 26 0 2 108 59 0 2 194
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101 chr1 30922 G T 999 0 23 0 66 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 2 0 3 0 14 0 39 14 16 1 153 0 45 0 132 6 0 2 48 19 0 2 87 3 0 2 32 0 0 -1 0 0 0 -1 0
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102 etc.
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103
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104 - text output::
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105
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106 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
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107 John West 0 0 0 0 0 0 0 0 1 1 1 1 2 2 3 3 4 4 5 6
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108 NA12892 0 2 5 11 20 31 43 55 67 77 84 90 93 96 97 98 99 99 99 99
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109 NA12891 0 0 0 0 0 1 1 2 3 5 6 9 11 15 19 23 29 35 41 47
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110 NA12249 1 4 11 23 38 54 68 79 88 93 96 98 99 99 99 99 99 99 99 99
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111 NA12342 0 0 1 1 2 4 6 9 13 18 23 29 36 43 50 58 65 71 77 82
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112 KB1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 2 2
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113 ABT 0 0 0 0 0 0 1 1 1 2 3 4 5 6 8 10 12 14 18 21
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114 NA18507 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
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115 NA19238 0 0 0 1 2 4 6 10 14 19 25 32 39 47 55 62 69 76 81 86
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116 NA19239 0 0 0 0 1 1 2 4 5 8 11 15 19 24 31 37 44 51 58 65
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117 YH 2 4 6 7 8 8 9 10 11 12 14 17 19 22 25 29 32 36 40 45
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118 KOREAN 0 0 1 1 3 4 5 7 10 12 15 19 22 27 31 37 42 48 54 60
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119 JPT 0 0 0 0 0 0 0 0 1 1 1 2 2 3 4 5 7 8 10 12
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120 etc.
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121
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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122 graphical output:
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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123
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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124 .. image:: ${static_path}/images/gd_coverage.png
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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125
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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126 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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127 </tool>