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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
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1 <tool id="gd_discover_familial_relationships" name="Close relatives" version="1.0.0">
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2 <description>: Discover familial relationships</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 discover_familial_relationships.py '$input' '$input.ext' '$ind_arg' '$pop_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="Input dataset" />
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19 <param name="pop_input" type="data" format="gd_indivs" label="Individuals dataset" />
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20 </inputs>
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21
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22 <outputs>
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23 <data name="output" format="tabular" />
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24 </outputs>
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25
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26 <requirements>
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27 <requirement type="package" version="0.1">gd_c_tools</requirement>
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28 </requirements>
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29
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30 <!--
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31 <tests>
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32 </tests>
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33 -->
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34
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35 <help>
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36
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37 **Dataset formats**
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38
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39 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
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40 The output dataset is in tabular_ format.
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41
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42 .. _gd_snp: ./static/formatHelp.html#gd_snp
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43 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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44 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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45 .. _tabular: ./static/formatHelp.html#tab
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46
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47 -----
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48
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49 **What it does**
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50
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51 The user specifies a SNP table (either gd_snp or gd_genotype format) and
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52 a set of individuals. The command runs the KING program (Manichaikul et
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53 al., 2010) to look for pairs of distinct individuals in the specified
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54 set that have a close family relationship. Putatively related pairs
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55 are classified into five categories:
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56
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57 1. duplicate or MZ twin
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58 2. 1st degree relatives -- siblings (other than identical twins) or parent-child
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59 3. 2nd degree relatives -- e.g., half-siblings, grandparent-grandchild pair, individual-uncle/aunt pair
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60 4. 3rd degree relatives -- e.g., first cousins
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61 5. unrelated
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62
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63 Reference:
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64
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65 Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in genome-wide association studies. Bioinformatics 26: 2867-2873.
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66 </help>
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67 </tool>