Mercurial > repos > iuc > gemini_roh

annotate gemini_roh.xml @ 6:60f477e3c79b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"
author iuc
date Fri, 24 Jan 2020 17:27:14 -0500
parents d65ca2fa673b
children e8349da26ed5
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Identifying runs of homozygosity</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">roh</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
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13 --min-snps $min_snps
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14 --min-total-depth $min_total_depth
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15 --min-gt-depth $min_gt_depth
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16 --min-size $min_size
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17 --max-hets $max_hets
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18 --max-unknowns $max_unknowns
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19 #if $samples.strip():
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20 #set $samples = ','.join([f.strip() for f in $samples.split(',')])
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21 -s '$samples'
0
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22 #end if
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23 '$infile'
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24 > '$outfile'
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25 ]]>
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26 </command>
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27 <inputs>
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28 <expand macro="infile" />
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29 <param argument="--min-snps" name="min_snps" type="integer" value="25" min="0"
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30 label="Minimum number of expected homozygous SNPs"
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31 help="default: 25" />
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32 <param argument="--min-total-depth" name="min_total_depth" type="integer" value="20" min="0"
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33 label="The minimum overall sequencing depth required for a SNP to be considered"
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34 help="default: 20" />
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35 <param argument="--min-gt-depth" name="min_gt_depth" type="integer" value="0" min="0"
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36 label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
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37 help="default: 0" />
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38 <param argument="--min-size" name="min_size" type="integer" value="100000" min="1"
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39 label="Minimum run size in base pairs" help="default: 100000" />
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40 <param argument="--max-hets" name="max_hets" type="integer" value="1" min="0"
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41 label="Maximum number of allowed hets in the run" help="default: 1" />
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42 <param argument="--max-unknowns" name="max_unknowns" type="integer" value="3" min="0"
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43 label="Maximum number of allowed unknowns in the run"
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44 help="default: 3" />
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45 <param argument="-s" name="samples" type="text" value=""
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46 label="Comma separated list of samples to screen for ROHs" help="e.g. S120,S450"/>
0
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47 </inputs>
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48 <outputs>
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49 <data name="outfile" format="tabular" />
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50 </outputs>
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51 <tests>
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52 <test>
4
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53 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
0
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54 <param name="min_snps" value="3" />
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55 <param name="min_size" value="10" />
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56 <param name="min_total_depth" value="0" />
4
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57 <output name="outfile">
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58 <assert_contents>
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59 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*run_length.*" />
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60 </assert_contents>
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61 </output>
0
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65
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66 **What it does**
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67
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68 Runs of homozygosity are long stretches of homozygous genotypes that reflect
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69 segments shared identically by descent and are a result of consanguinity or
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70 natural selection. Consanguinity elevates the occurrence of rare recessive
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71 diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious
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72 mutations. Hence, the identification of these runs holds medical value.
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73
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74 The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data.
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75 The tool basically looks at every homozygous position on the chromosome as a possible
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76 start site for the run and looks for those that could give rise to a potentially long
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77 stretch of homozygous genotypes.
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78
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79 For e.g. for the given example allowing ``1 HET`` genotype (h) and ``2 UKW`` genotypes (u)
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80 the possible roh runs (H) would be:
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81
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82
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83 ::
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84
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85 genotype_run = H H H H h H H H H u H H H H H u H H H H H H H h H H H H H h H H H H H
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86 roh_run1 = H H H H h H H H H u H H H H H u H H H H H H H
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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87 roh_run2 = H H H H u H H H H H u H H H H H H H h H H H H H
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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88 roh_run3 = H H H H H u H H H H H H H h H H H H H
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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89 roh_run4 = H H H H H H H h H H H H H
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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90
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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91 roh returned for --min-snps = 20 would be:
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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92
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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93 ::
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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94
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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95 roh_run1 = H H H H h H H H H u H H H H H u H H H H H H H
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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96 roh_run2 = H H H H u H H H H H u H H H H H H H h H H H H H
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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97
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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98
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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99 As you can see, the immediate homozygous position right of a break (h or u) would be the possible
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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100 start of a new roh run and genotypes to the left of a break are pruned since they cannot
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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101 be part of a longer run than we have seen before.
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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102
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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103
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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104 ]]></help>
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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105 <expand macro="citations"/>
91b4db3e6df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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106 </tool>