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annotate dpmix.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
parents d6b961721037
children cba0d7a63b82
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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 ancestral populations</description>
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3
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4 <command interpreter="python">
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5 dpmix.py "$input"
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6 #if $input_type.choice == '0'
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7 "gd_snp" "$input_type.data_source"
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8 #else if $input_type.choice == '1'
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9 "gd_genotype" "1"
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10 #end if
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11 "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
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12 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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13 #set $arg = '%s:%s' % ($individual_col, $individual)
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14 "$arg"
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15 #end for
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16 </command>
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17
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18 <inputs>
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19 <conditional name="input_type">
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20 <param name="choice" type="select" format="integer" label="Input format">
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21 <option value="0" selected="true">gd_snp</option>
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22 <option value="1">gd_genotype</option>
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23 </param>
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24 <when value="0">
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25 <param name="input" type="data" format="gd_snp" label="SNP dataset">
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26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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27 </param>
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29 <param name="data_source" type="select" format="integer" label="Similarity metric">
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30 <option value="0">sequence coverage</option>
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31 <option value="1" selected="true">estimated genotype</option>
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32 </param>
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33 </when>
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34 <when value="1">
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35 <param name="input" type="data" format="gd_genotype" label="Genotype dataset">
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36 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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37 </param>
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38 </when>
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39 </conditional>
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40
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41 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" />
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42 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" />
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43 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />
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44
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45 <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/>
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46 </inputs>
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47
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48 <outputs>
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49 <data name="output" format="tabular" />
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50 <data name="output2" format="html" />
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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56 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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57 <param name="ap2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" />
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58 <param name="p_input" value="test_in/c.gd_indivs" ftype="gd_indivs" />
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59 <param name="data_source" value="0" />
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60 <param name="switch_penalty" value="10" />
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61
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62 <output name="output" file="test_out/dpmix/dpmix.tabular" />
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63
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64 <output name="output2" file="test_out/dpmix/dpmix.html" ftype="html" compare="diff" lines_diff="2">
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65 <extra_files type="file" name="dpmix.pdf" value="test_out/dpmix/dpmix.pdf" compare="sim_size" delta = "10000" />
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66 <extra_files type="file" name="misc.txt" value="test_out/dpmix/misc.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 datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats. It is important for
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76 the Individuals datasets to have unique names and for there to be no overlap
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77 between the two populations. Rename these datasets if
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78 needed to make them unique.
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79 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_)
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80
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81 .. _gd_snp: ./static/formatHelp.html#gd_snp
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82 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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83 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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84 .. _tabular: ./static/formatHelp.html#tab
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85 .. _Dataset missing?: ./static/formatHelp.html
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86
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87 -----
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88
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89 **What it does**
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90
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91 The user specifies two "ancestral" populations (i.e., sources for
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92 chromosomes) and a set of potentially admixed individuals, and chooses
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93 between the sequence coverage or the estimated genotypes to measure
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94 the similarity of genomic intervals in admixed individuals to the two
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95 classes of ancestral chromosomes. The user also picks a "genotype switch penalty",
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96 typically between 10 and 100. For each potentially admixed individual,
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97 the program divides the genome into three "genotypes": (0) homozygous
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98 for the first ancestral population (i.e., both chromosomes from that
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99 population), (1) heterozygous, or (2) homozygous for the second ancestral
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100 population. Parts of a chromosome that are labeled as "heterochromatic"
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101 are given the non-genotype "3". Smaller values of the switch penalty
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102 (corresponding to more ancient admixture events) generally lead to the
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103 reconstruction of more frequent changes between genotypes.
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104
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105 There are two output datasets generated. A tabular dataset with chromosome,
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106 start, stop, and pairs of columns containing the "genotypes" from above
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107 and label from the admixed individual. The second dataset is a composite
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108 dataset with general information from the run and a link to a pdf which
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109 graphically shows the ancestral population along each of the chromosomes.
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110 The second link is to a text file with summary information of the
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111 "genotypes" over the whole genome.
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112
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113 </help>
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114 </tool>