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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2
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2 <description>Querying the GEMINI database</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">query</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 gemini @BINARY@
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12
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13 --in "${in}"
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14
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15 #if $gt_filter.strip():
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16 --gt-filter "${gt_filter}"
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17 #end if
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18
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19 #if $sample_filter.strip():
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20 --sample-filter "${sample_filter}"
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21 #end if
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22
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23 $show_samples
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24 $show_families
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25 $family_wise
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26 $header
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27 $dgidb
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28 #if $region.strip():
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29 --region "${region}"
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30 #end if
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31 #if int($min_kindreds) > 0:
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32 --min-kindreds $min_kindreds
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33 #end if
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34 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
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35 ## --sample-delim STRING The delimiter to be used with the --show-samples option.
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36
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37 #if $q.strip():
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38 -q "${q}"
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39 #end if
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40
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41 "${ infile }"
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42 > "${ outfile }"
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43 ]]>
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44 </command>
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45 <!--
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46 ##TODO:
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47 - -carrier-summary-by-phenotype CARRIER_SUMMARY
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48 Output columns of counts of carriers and non-carriers
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49 stratified by the given sample phenotype column-->
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50 <expand macro="stdio" />
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51 <inputs>
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52 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
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53
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54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"/>
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55 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"/>
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56 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"/>
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57
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58 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False"
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59 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
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60
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61 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False"
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62 label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>
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63
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64 <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
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65 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>
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66
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67 <expand macro="add_header_column" />
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68
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69 <!-- TODO: is there any default values set? -->
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70 <param name="min_kindreds" size="4" type="integer" value="-1" lebel="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" />
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71
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72 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
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73 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
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74
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75 <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)">
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76 <option value="all">Return a variant if all samples matching the query have the variant. (all)</option>
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77 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
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78 <option value="any">Return all of the variant which are in all of the matching samples and not in any of the non-matching samples. (any)</option>
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79 <option value="only">Return a variant if the variant is only in the matching samples and not in any of the non-matching samples. (only)</option>
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80 </param>
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81
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82 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
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83
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84
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85 </inputs>
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86 <outputs>
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87 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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88 </outputs>
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89 <tests>
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90 <test>
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91 </test>
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92 </tests>
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93 <help>
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94 **What it does**
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95
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96 The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation.
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97 The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants!
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98
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99 http://gemini.readthedocs.org/en/latest/content/querying.html
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100
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101 @CITATION@
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102 </help>
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103 <expand macro="citations"/>
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104 </tool>
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