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annotate offspring_heterozygosity_pedigree.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_offspring_heterozygosity_pedigree" name="Founders sequenced" version="1.0.0">
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2 <description>: Offspring estimated heterozygosity from a pedigree with sequenced founders</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 offspring_heterozygosity_pedigree.py '$input' '$input.ext' '$pedigree' '$ind_arg' '$founders' '$b1_input' '$b2_input' '$output'
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15 </command>
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16
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17 <inputs>
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18 <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP dataset" />
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19 <param name="pedigree" type="data" format="txt" label="Pedigree dataset" />
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20 <param name="founders" type="data" format="gd_indivs" label="Founders dataset" />
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21 <param name="b1_input" type="data" format="txt" label="First breeders dataset" />
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22 <param name="b2_input" type="data" format="txt" label="Second breeders dataset" />
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23 </inputs>
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24
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25 <outputs>
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26 <data name="output" format="txt" />
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27 </outputs>
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28
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29 <requirements>
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30 <requirement type="package" version="0.1">gd_c_tools</requirement>
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31 </requirements>
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32
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33 <!--
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34 <tests>
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35 </tests>
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36 -->
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37
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38 <help>
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39
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40 **Dataset formats**
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41
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42 The input datasets are in gd_snp_, gd_genotype_, text_, and gd_indivs_ formats.
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43 The output dataset is in text_ format.
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44
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45 .. _gd_snp: ./static/formatHelp.html#gd_snp
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46 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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47 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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48 .. _text: ./static/formatHelp.html#text
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49
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50 -----
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51
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52 **What it does**
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53
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54 The user provides a Galaxy SNP table (gd_snp or gd_genotype format) that
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55 includes the founders of a pedigree, as well as two sets of individuals.
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56 The pedigree is specified by a text file with one row per individual,
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57 containing (1) the individual's name, (2) the name of one of the
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58 individual's parents, which must have occurred at the start of a previous
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59 line, and (3) the name of the individual's other parent, which occurred at
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60 the start of a previous line. For a pedigree founder, both parent names
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61 are replaced by &quot;-&quot;. The founders are specified by a table in
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62 gd_indivs format, e.g., as produced by &quot;Specify individuals&quot;
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63 tool. Every founder must have genotypes supplied in the SNP table,
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64 and both parents need to be given as &quot;-&quot; in the pedigree.
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65 Conversely, every pedigree individual whose parents are &quot;-&quot;
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66 must be named as a founder.
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67
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68 The user also provides two files that specify a set of names of
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69 individuals. The first word on each line names an individual (one
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70 line per individual); any subsequent information on a line is ignored.
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71 The name of each individual must appear at the start of a line in the
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72 pedigree.
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73
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74 For each pair of individuals, one from each specified set, the program
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75 computes the expected heterozygosity of any offspring of the pair,
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76 i.e., the probability that the offspring has distinct nucleotides at
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77 a randomly chosen autosomal SNP. A SNP is ignorned if one or both
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78 potential parents have an ancestor with undefined genotype (designated
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79 as -1 in the SNP table).
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80 </help>
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81 </tool>