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annotate prepare_population_structure.xml @ 14:8ae67e9fb6ff

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Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
author miller-lab
date Fri, 28 Sep 2012 11:35:56 -0400
parents
children f04f40a36cc8
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14
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1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.0.0">
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2 <description>: Filter and convert to the format needed for these tools</description>
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3
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4 <command interpreter="python">
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5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
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6 #if $individuals.choice == '0'
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7 "all_individuals"
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8 #else if $individuals.choice == '1'
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9 #for $population in $individuals.populations
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10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
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11 "$pop_arg"
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12 #end for
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13 #end if
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14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
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16 "$arg"
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17 #end for
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18 </command>
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19
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20 <inputs>
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21 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" />
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23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" />
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24 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" />
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25 <conditional name="individuals">
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26 <param name="choice" type="select" label="Individuals">
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27 <option value="0" selected="true">All</option>
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28 <option value="1">Choose</option>
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29 </param>
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30 <when value="0" />
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31 <when value="1">
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32 <repeat name="populations" title="Population" min="1">
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33 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
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34 </repeat>
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35 </when>
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36 </conditional>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="output" format="gd_ped">
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41 <actions>
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42 <action type="metadata" name="base_name" default="admix" />
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43 </actions>
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44 </data>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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50 <param name="min_reads" value="3" />
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51 <param name="min_qual" value="30" />
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52 <param name="min_spacing" value="0" />
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53 <param name="choice" value="0" />
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54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
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55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
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56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
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57 </output>
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58 </test>
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59 </tests>
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60
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61 <help>
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62
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63 **Dataset formats**
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64
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65 The input datasets are in gd_snp_ and gd_indivs_ formats. It is important
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66 for the Individuals datasets to have unique names; rename them if
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67 necessary to make them unique. These names are used by the later tools in
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68 the graphical displays.
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69 The output dataset is gd_ped_. (`Dataset missing?`_)
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70
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71 .. _gd_snp: ./static/formatHelp.html#gd_snp
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72 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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73 .. _gd_ped: ./static/formatHelp.html#gd_ped
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74 .. _Dataset missing?: ./static/formatHelp.html
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75
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76 -----
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77
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78 **What it does**
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79
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80 The tool converts a gd_snp dataset into two tables, called "admix.map" and
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81 "admix.ped", needed for estimating the population structure. The user
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82 can read or download those files, or simply pass this tool's output on to
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83 other programs. The user imposes conditions on which SNPs to consider,
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84 such as the minimum coverage and/or quality value for every individual,
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85 or the distance to the closest SNP in the same contig (as named in the
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86 first column of the SNP table). A useful piece of information produced
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87 by the tool is the number of SNPs meeting those conditions, which can
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88 be found by clicking on the eye icon in the history panel after the program
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89 runs.
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90
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91 -----
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92
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93 **Example**
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94
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95 - input::
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96
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97 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
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98 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0
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99 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0
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100 etc.
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101
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102 - output map file::
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103
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104 1 snp1 0 2
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105 1 snp3 0 4
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106 1 snp4 0 5
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107 1 snp5 0 6
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108 1 snp6 0 7
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109 1 snp7 0 8
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110 1 snp8 0 9
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111 1 snp9 0 10
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112
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113 - output ped file::
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114
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115 PB1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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116
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
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117 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
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118 </tool>