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annotate dpmix.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 4188853b940b
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1 <tool id="gd_dpmix" name="Admixture" version="1.1.0">
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2 <description>: Map genomic intervals resembling specified source populations</description>
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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 dpmix.py '$input'
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15 #if $input_type.choice == '0'
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16 'gd_snp' '$input_type.data_source'
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17 #else if $input_type.choice == '1'
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18 'gd_genotype' '1'
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19 #end if
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20 #if $third_pop.choice == '0'
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21 #set $ap3_arg = '/dev/null'
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22 #set $ap3_name_arg = ''
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23 #else if $third_pop.choice == '1'
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24 #set $ap3_arg = $third_pop.ap3_input
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25 #set $ap3_name_arg = $third_pop.ap3_input.name
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26 #end if
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27 #if $user_het.choice == '0'
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28 #set $het_arg = 'use_installed'
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29 #else if $user_het.choice == '1'
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30 #set $het_arg = $user_het.het_file
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31 #else if $user_het.choice == '2'
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32 #set $het_arg = 'use_none'
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33 #end if
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34 '$switch_penalty' '$ap1_input' '$ap1_input.name' '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '1'
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35 </command>
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37 <inputs>
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38 <conditional name="input_type">
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39 <param name="choice" type="select" format="integer" label="Input format">
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40 <option value="0" selected="true">gd_snp</option>
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41 <option value="1">gd_genotype</option>
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42 </param>
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43 <when value="0">
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44 <param name="input" type="data" format="gd_snp" label="SNP dataset">
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45 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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46 </param>
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47
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48 <param name="data_source" type="select" format="integer" label="Similarity metric">
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49 <option value="0">sequence coverage</option>
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50 <option value="1" selected="true">estimated genotype</option>
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51 </param>
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52 </when>
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53 <when value="1">
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54 <param name="input" type="data" format="gd_genotype" label="Genotype dataset">
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55 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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56 </param>
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57 </when>
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58 </conditional>
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59
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60 <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" />
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61 <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" />
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62
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63 <conditional name="third_pop">
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64 <param name="choice" type="select" format="integer" label="Include third source population">
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65 <option value="0" selected="true">no</option>
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66 <option value="1">yes</option>
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67 </param>
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68 <when value="0" />
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69 <when value="1">
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70 <param name="ap3_input" type="data" format="gd_indivs" label="Source population 3 individuals" />
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71 </when>
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72 </conditional>
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73
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74 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />
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75
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76 <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note: Depends on the density of SNPs. For instance, with 50,000 SNPs in a vertebrate genome, 1.0 might be appropriate, with millions of SNPs, a value between 10 and 100 might be reasonable."/>
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78 <conditional name="user_het">
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79 <param name="choice" type="select" format="integer" label="Heterochromatin info">
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80 <option value="0" selected="true">use installed</option>
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81 <option value="1">use your own</option>
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82 <option value="2">use none</option>
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83 </param>
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84 <when value="0" />
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85 <when value="1">
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86 <param name="het_file" type="data" format="txt" label="Heterochromatin dataset" />
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87 </when>
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88 </conditional>
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90 <!--
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91 <param name="add_logs" type="select" format="integer" label="Probabilities">
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92 <option value="1" selected="true">add logs of probabilities</option>
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93 <option value="0">add probabilities</option>
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94 </param>
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95 -->
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96
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97 </inputs>
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98
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99 <outputs>
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100 <data name="output" format="tabular" />
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101 <data name="output2" format="html" />
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102 </outputs>
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103
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104 <tests>
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105 <test>
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106 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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107 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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108 <param name="ap2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" />
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109 <param name="p_input" value="test_in/c.gd_indivs" ftype="gd_indivs" />
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110 <param name="data_source" value="0" />
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111 <param name="switch_penalty" value="10" />
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112
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113 <output name="output" file="test_out/dpmix/dpmix.tabular" />
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114
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115 <output name="output2" file="test_out/dpmix/dpmix.html" ftype="html" compare="diff" lines_diff="2">
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116 <extra_files type="file" name="dpmix.pdf" value="test_out/dpmix/dpmix.pdf" compare="sim_size" delta = "10000" />
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117 <extra_files type="file" name="misc.txt" value="test_out/dpmix/misc.txt" />
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118 </output>
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119 </test>
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120 </tests>
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121
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122 <help>
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123
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124 **Dataset formats**
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125
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126 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats. It is important for
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127 the Individuals datasets to have unique names and for there to be no overlap
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128 between the two populations. Rename these datasets if
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129 needed to make them unique.
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130 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_)
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131
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132 .. _gd_snp: ./static/formatHelp.html#gd_snp
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133 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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134 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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135 .. _tabular: ./static/formatHelp.html#tab
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136 .. _Dataset missing?: ./static/formatHelp.html
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137
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138 -----
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139
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140 **What it does**
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141
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142 The user specifies two or three source populations (i.e., sources
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143 for chromosomes) and a set of potentially admixed individuals, and
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144 chooses between the sequence coverage or the estimated genotypes to
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145 measure the similarity of genomic intervals in admixed individuals to
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146 the three classes of source chromosomes. The user also specifies a
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147 "switch penalty", controlling the strength of evidence needed to switch
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148 between source populations as the the program scans along a chromosome.
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149 Choice of picksan appropriate value depends on the number of SNPs and, to
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150 a lesser extent, on the time since the admixture events. With several
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151 million SNPs genome-wide, reasonable values might fall between 10
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152 and 100. If there are 3 source populatons, then for each potentially
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153 admixed individual the program divides the genome into six "genotypes":
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154
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155 1. homozygous for the first source population (i.e., both chromosomes from that population),
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156 2. homozygous for the second source population,
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157 3. homozygous for the third source population,
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158 4. heterozygous for the first and second populations (i.e., one chromosome from each),
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159 5. heterozygous for the first and third populations, or
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160 6. heterozygous for the second and third populations.
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161
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162 Parts of a reference chromosome that are labeled as "heterochromatic"
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163 are given the "non-genotype" 0. With two source populations, only
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164 "genotypes" 1, 2 and 3 are possible, where 3 now means heterozygous in
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165 the two source populations.
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166
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167 There are two output datasets generated. A tabular dataset with chromosome,
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168 start, stop, and pairs of columns containing the "genotypes" from above
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169 and label from the admixed individual. The second dataset is a composite
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170 dataset with general information from the run and a link to a pdf which
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171 graphically shows the source population along each of the chromosomes.
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172 The second link is to a text file with summary information of the
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173 "genotypes" over the whole genome.
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174 </help>
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175 </tool>